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/7921156/working' mkdir: created directory `/scratch/stefan/7921156/working/protonate' Storing results in /scratch/stefan/7921156/finished Working in /scratch/stefan/7921156/working /scratch/stefan/7921156/working /scratch/stefan/7921156 /scratch/stefan/7921156/working/protonate /scratch/stefan/7921156/working /scratch/stefan/7921156 Precomputing protomers for all compounds (pH: 7.4) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (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 awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (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 rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory 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 awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (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 awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory 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 awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory chmod: cannot access `/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 awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (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: 1081 protomers created Coalesing and merging protomers 1038 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1053 protomers after new stereo-center expansion /scratch/stefan/7921156/working /scratch/stefan/7921156 Bulk generating 3D conformations all protomers in /scratch/stefan/7921156/working/3D mkdir: created directory `/scratch/stefan/7921156/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7921156/working/protonate/xaaaaao-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' 1054 3D conformations generated for 1000 compounds Building REAL250005051893 mkdir: created directory `/scratch/stefan/7921156/working/building' mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051893' /scratch/stefan/7921156/working/building/REAL250005051893 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051893 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051893/0 /scratch/stefan/7921156/working/building/REAL250005051893 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1 `/scratch/stefan/7921156/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=NC=N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051893.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051893 none CC(CNC(=O)C1=CC=NC=N1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [64, 40, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 64, 75, 75, 75, 77, 77, 77, 77, 77, 64, 64, 64, 64, 40, 40, 12, 1, 1, 1, 75, 77] 77 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32]) total number of confs: 292 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: REAL250005051893 none CC(CNC(=O)C1=CC=NC=N1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 14, 26, 54, 54, 54, 77, 77, 77, 77, 77, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 26, 26, 54, 77, 77, 77, 7, 1] 77 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: 221 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051893 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051893 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `/scratch/stefan/7921156/finished' Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051893/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051893 Building REAL250005051894 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051894' /scratch/stefan/7921156/working/building/REAL250005051894 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051894 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051894/0 /scratch/stefan/7921156/working/building/REAL250005051894 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/2 `/scratch/stefan/7921156/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1=CC=CO1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051894.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051894 none CC(CNC(=O)CC1=CC=CO1)NC(=O)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.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 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, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 124, 33, 33, 5, 33, 1, 1, 1, 1, 1, 1, 183, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 183, 183, 124, 124, 33, 5, 5, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 30, 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, 33, 34]) total number of confs: 845 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: REAL250005051894 none CC(CNC(=O)CC1=CC=CO1)NC(=O)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.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 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, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 10, 25, 65, 65, 65, 153, 201, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 25, 25, 65, 153, 153, 201, 201, 201, 4, 1] 201 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 650 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051894 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051894 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051894/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051894 Building REAL250005051895 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051895' /scratch/stefan/7921156/working/building/REAL250005051895 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051895 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051895/0 /scratch/stefan/7921156/working/building/REAL250005051895 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/3 `/scratch/stefan/7921156/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=NC=CC=N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051895.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051895 none CC(CNC(=O)C1=NC=CC=N1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [44, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 44, 49, 49, 49, 52, 52, 52, 52, 52, 44, 44, 44, 44, 30, 30, 11, 1, 1, 1, 49, 52] 52 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32]) 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: REAL250005051895 none CC(CNC(=O)C1=NC=CC=N1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 14, 27, 48, 48, 48, 52, 52, 48, 52, 52, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 27, 27, 48, 52, 48, 52, 7, 1] 52 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: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051895 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051895 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051895/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051895 Building REAL250005051896 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051896' /scratch/stefan/7921156/working/building/REAL250005051896 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051896 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051896/0 /scratch/stefan/7921156/working/building/REAL250005051896 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/4 `/scratch/stefan/7921156/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051896.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051896 none CCC(C)CCC(=O)NCC(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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 195, 136, 195, 117, 33, 33, 33, 19, 8, 4, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 196, 196, 195, 196, 153, 153, 117, 117, 33, 19, 19, 8, 8, 8, 8, 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: 1002 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051896 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051896 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051896/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051896 Building REAL250005051897 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051897' /scratch/stefan/7921156/working/building/REAL250005051897 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051897 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051897/0 /scratch/stefan/7921156/working/building/REAL250005051897 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/5 `/scratch/stefan/7921156/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=CN=N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051897.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051897 none CC(CNC(=O)C1=CC=CN=N1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [81, 45, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 81, 98, 98, 98, 106, 106, 106, 106, 106, 81, 81, 81, 81, 45, 45, 12, 1, 1, 1, 98, 106] 106 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32]) total number of confs: 405 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: REAL250005051897 none CC(CNC(=O)C1=CC=CN=N1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 15, 37, 73, 73, 73, 106, 106, 106, 106, 106, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 37, 37, 73, 106, 106, 106, 8, 1] 106 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: 314 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051897 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051897 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051897/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051897 Building REAL250005051898 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051898' /scratch/stefan/7921156/working/building/REAL250005051898 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051898 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051898/0 /scratch/stefan/7921156/working/building/REAL250005051898 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/6 `/scratch/stefan/7921156/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCOC1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051898.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051898 none CC(CNC(=O)C1CCOC1C)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 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, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [45, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 68, 68, 68, 71, 71, 71, 71, 71, 45, 45, 45, 45, 14, 14, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 68, 71] 71 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 28, 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, 34, 35, 36, 37, 38]) total number of confs: 268 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: REAL250005051898 none CC(CNC(=O)C1CCOC1C)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 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, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 46, 68, 68, 68, 71, 71, 71, 71, 71, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 46, 46, 68, 71, 71, 71, 71, 71, 71, 71, 71, 71, 8, 1] 71 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: 259 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051898 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051898 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051898/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051898 Building REAL250005051899 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051899' /scratch/stefan/7921156/working/building/REAL250005051899 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051899 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051899/0 /scratch/stefan/7921156/working/building/REAL250005051899 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/7 `/scratch/stefan/7921156/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(C)CCOC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051899.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051899 none CC(CNC(=O)C1(C)CCOC1)NC(=O)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'] 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, 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, 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: [103, 31, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 104, 152, 153, 152, 158, 158, 158, 158, 158, 104, 104, 104, 104, 31, 31, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 153, 158] 158 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 36, 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, 30, 37, 38]) total number of confs: 608 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051899 none CC(CNC(=O)C1(C)CCOC1)NC(=O)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'] 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, 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, 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: [16, 7, 16, 50, 101, 101, 101, 158, 158, 158, 158, 158, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 101, 158, 158, 158, 158, 158, 158, 158, 158, 158, 7, 1] 158 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: 540 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051899 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051899 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051899/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051899 Building REAL250005051900 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051900' /scratch/stefan/7921156/working/building/REAL250005051900 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051900 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051900/0 /scratch/stefan/7921156/working/building/REAL250005051900 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/8 `/scratch/stefan/7921156/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051900.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051900 none CCC(CC)CC(=O)NCC(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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 168, 121, 172, 191, 34, 34, 34, 25, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 193, 193, 193, 190, 191, 173, 191, 190, 191, 191, 191, 121, 121, 34, 25, 25, 12, 12, 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: 971 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051900 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051900 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051900/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051900 Building REAL250005051901 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051901' /scratch/stefan/7921156/working/building/REAL250005051901 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051901 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051901/0 /scratch/stefan/7921156/working/building/REAL250005051901 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/9 `/scratch/stefan/7921156/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051901.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051901 none CCC(C)C(C)C(=O)NCC(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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 185, 155, 186, 77, 155, 77, 77, 49, 23, 9, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 198, 187, 187, 187, 187, 155, 155, 155, 155, 77, 49, 49, 23, 23, 23, 23, 9, 1] 199 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: 899 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051901 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051901 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051901/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051901 Building REAL250005051902 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051902' /scratch/stefan/7921156/working/building/REAL250005051902 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051902 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051902/0 /scratch/stefan/7921156/working/building/REAL250005051902 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/10 `/scratch/stefan/7921156/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CC)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051902.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051902 none CCCC(CC)C(=O)NCC(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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 178, 130, 55, 130, 145, 55, 55, 35, 15, 5, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 193, 193, 193, 190, 193, 183, 183, 130, 157, 157, 157, 157, 157, 55, 35, 35, 15, 15, 15, 15, 5, 1] 201 rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1124 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051902 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051902 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051902/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051902 Building REAL250005051903 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051903' /scratch/stefan/7921156/working/building/REAL250005051903 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051903 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051903/0 /scratch/stefan/7921156/working/building/REAL250005051903 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/11 `/scratch/stefan/7921156/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCC(F)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051903.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051903 none CC(CNC(=O)C1CCC(F)C1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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: [149, 57, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 150, 194, 194, 194, 201, 201, 201, 201, 201, 150, 150, 150, 150, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 194, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 28, 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, 36, 37]) total number of confs: 795 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: REAL250005051903 none CC(CNC(=O)C1CCC(F)C1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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: [22, 10, 22, 60, 124, 124, 124, 201, 201, 201, 201, 201, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 60, 60, 124, 201, 201, 201, 201, 201, 201, 201, 201, 10, 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: 661 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051903 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051903 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051903/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051903 Building REAL250005051904 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051904' /scratch/stefan/7921156/working/building/REAL250005051904 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051904 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051904/0 /scratch/stefan/7921156/working/building/REAL250005051904 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/12 `/scratch/stefan/7921156/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051904.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051904 none C=CCCCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 116, 122, 38, 38, 38, 16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 187, 186, 145, 145, 122, 122, 38, 16, 16, 8, 8, 8, 8, 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: 984 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051904 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051904 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051904/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051904 Building REAL250005051905 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051905' /scratch/stefan/7921156/working/building/REAL250005051905 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051905 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051905/0 /scratch/stefan/7921156/working/building/REAL250005051905 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/13 `/scratch/stefan/7921156/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051905.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051905 none CCC(C)(C)C(=O)NCC(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [152, 148, 81, 148, 148, 81, 81, 48, 22, 10, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 170, 148, 148, 148, 148, 148, 148, 81, 48, 48, 22, 22, 22, 22, 10, 1] 170 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: 842 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051905 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051905 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051905/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051905 Building REAL250005051906 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051906' /scratch/stefan/7921156/working/building/REAL250005051906 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051906 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051906/0 /scratch/stefan/7921156/working/building/REAL250005051906 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/14 `/scratch/stefan/7921156/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051906.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051906 none CCCC(C)(C)C(=O)NCC(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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 162, 111, 162, 162, 111, 111, 44, 16, 4, 16, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 162, 162, 162, 162, 162, 162, 111, 44, 44, 16, 16, 16, 16, 4, 1] 201 rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 839 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051906 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051906 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051906/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051906 Building REAL250005051907 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051907' /scratch/stefan/7921156/working/building/REAL250005051907 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051907 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051907/0 /scratch/stefan/7921156/working/building/REAL250005051907 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/15 `/scratch/stefan/7921156/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(C(N)=O)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051907.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051907 none CC(CNC(=O)C1(C(N)=O)CC1)NC(=O)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', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 11, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 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: [108, 41, 7, 7, 1, 7, 1, 1, 7, 7, 1, 1, 108, 168, 168, 168, 173, 173, 173, 173, 173, 108, 108, 108, 108, 41, 41, 7, 7, 7, 1, 1, 1, 1, 168, 173] 201 rigid atoms, others: [32, 33, 4, 6, 7, 10, 11, 30, 31] set([0, 1, 2, 3, 5, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 663 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: REAL250005051907 none CC(CNC(=O)C1(C(N)=O)CC1)NC(=O)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', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 11, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 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: [12, 6, 12, 33, 90, 90, 90, 173, 201, 201, 173, 173, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 33, 33, 90, 201, 201, 173, 173, 173, 173, 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: 634 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051907 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051907 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051907/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051907 Building REAL250005051908 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051908' /scratch/stefan/7921156/working/building/REAL250005051908 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051908 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051908/0 /scratch/stefan/7921156/working/building/REAL250005051908 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/16 `/scratch/stefan/7921156/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(N)=O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051908.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051908 none 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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7] dock color type numbers: [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] 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: [15, 10, 15, 27, 51, 51, 51, 65, 66, 10, 1, 10, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 27, 27, 51, 66, 65, 10, 1] 66 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051908 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051908 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051908/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051908 Building REAL250005051909 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051909' /scratch/stefan/7921156/working/building/REAL250005051909 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051909 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051909/0 /scratch/stefan/7921156/working/building/REAL250005051909 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/17 `/scratch/stefan/7921156/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC=C1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051909.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051909 none CC1=NOC=C1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 44, 83, 84, 98, 98, 98, 101, 101, 101, 101, 101, 2, 2, 2, 1, 11, 44, 44, 84, 84, 84, 84, 98, 101] 101 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 410 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: REAL250005051909 none CC1=NOC=C1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 101, 76, 76, 76, 39, 15, 8, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 76, 39, 39, 15, 15, 15, 15, 8, 1] 101 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: 300 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051909 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051909 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051909/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051909 Building REAL250005051910 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051910' /scratch/stefan/7921156/working/building/REAL250005051910 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051910 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051910/0 /scratch/stefan/7921156/working/building/REAL250005051910 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/18 `/scratch/stefan/7921156/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C)CC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051910.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051910 none CCC1(C)CC1C(=O)NCC(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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 36, 109, 111, 169, 169, 169, 188, 188, 188, 188, 188, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 7, 36, 36, 111, 111, 111, 111, 169, 188] 199 rigid atoms, others: [1, 2, 3, 4, 5, 6, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 699 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: REAL250005051910 none CCC1(C)CC1C(=O)NCC(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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 188, 188, 188, 188, 131, 131, 131, 61, 23, 11, 23, 11, 1, 11, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 199, 188, 188, 188, 188, 188, 188, 131, 61, 61, 23, 23, 23, 23, 11, 1] 199 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 724 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051910 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051910 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051910/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051910 Building REAL250005051911 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051911' /scratch/stefan/7921156/working/building/REAL250005051911 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051911 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051911/0 /scratch/stefan/7921156/working/building/REAL250005051911 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/19 `/scratch/stefan/7921156/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051911.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051911 none COCC(C)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 93, 150, 22, 22, 22, 17, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 152, 152, 152, 152, 93, 93, 22, 17, 17, 11, 11, 11, 11, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 976 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051911 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051911 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051911/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051911 Building REAL250005051912 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051912' /scratch/stefan/7921156/working/building/REAL250005051912 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051912 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051912/0 /scratch/stefan/7921156/working/building/REAL250005051912 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/20 `/scratch/stefan/7921156/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCC1(C)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051912.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051912 none CC(CNC(=O)CCC1(C)CC1)NC(=O)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: [186, 120, 34, 34, 7, 34, 5, 1, 1, 1, 1, 1, 186, 201, 201, 201, 201, 201, 201, 201, 201, 187, 187, 186, 187, 122, 122, 34, 7, 7, 5, 5, 2, 2, 2, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 880 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: REAL250005051912 none CC(CNC(=O)CCC1(C)CC1)NC(=O)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: [9, 4, 9, 25, 63, 63, 63, 158, 159, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 25, 25, 63, 158, 158, 166, 166, 201, 201, 201, 201, 201, 201, 201, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 830 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051912 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051912 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051912/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051912 Building REAL250005051913 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051913' /scratch/stefan/7921156/working/building/REAL250005051913 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051913 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051913/0 /scratch/stefan/7921156/working/building/REAL250005051913 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/21 `/scratch/stefan/7921156/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)ON=C1) `REAL250005051913.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051913 none CC1=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)ON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 33, 89, 91, 122, 122, 122, 129, 129, 129, 129, 129, 1, 1, 1, 2, 2, 2, 8, 33, 33, 91, 91, 91, 91, 122, 129, 1] 129 rigid atoms, others: [0, 1, 2, 3, 33, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 503 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051913 none CC1=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)ON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 117, 117, 117, 63, 24, 9, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 129, 117, 63, 63, 24, 24, 24, 24, 9, 1, 129] 129 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 428 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051913 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051913 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051913/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051913 Building REAL250005051914 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051914' /scratch/stefan/7921156/working/building/REAL250005051914 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051914 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051914/0 /scratch/stefan/7921156/working/building/REAL250005051914 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/22 `/scratch/stefan/7921156/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(C)CC=CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051914.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051914 none CC(CNC(=O)C1(C)CC=CC1)NC(=O)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.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 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: [119, 35, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 122, 188, 190, 188, 201, 201, 201, 201, 201, 122, 122, 122, 122, 35, 35, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 190, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 36, 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, 30, 37, 38]) total number of confs: 768 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: REAL250005051914 none CC(CNC(=O)C1(C)CC=CC1)NC(=O)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.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 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: [20, 8, 20, 59, 126, 126, 126, 201, 201, 201, 201, 201, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 59, 59, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 8, 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: 672 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051914 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051914 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051914/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051914 Building REAL250005051915 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051915' /scratch/stefan/7921156/working/building/REAL250005051915 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051915 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051915/0 /scratch/stefan/7921156/working/building/REAL250005051915 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/23 `/scratch/stefan/7921156/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005051915.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051915 none COC(C(=O)NCC(C)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [175, 157, 115, 115, 115, 46, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 157, 200, 200, 175, 175, 175, 157, 115, 46, 46, 13, 13, 13, 13, 4, 1, 200, 200, 200, 200, 200, 200, 200] 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: 876 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051915 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051915 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051915/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051915 Building REAL250005051916 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051916' /scratch/stefan/7921156/working/building/REAL250005051916 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051916 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051916/0 /scratch/stefan/7921156/working/building/REAL250005051916 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/24 `/scratch/stefan/7921156/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CC1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051916.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051916 none CC(CNC(=O)CC1CC1C)NC(=O)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: [180, 133, 44, 44, 6, 44, 1, 1, 1, 1, 1, 180, 201, 201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 180, 133, 133, 44, 6, 6, 1, 1, 1, 1, 2, 2, 2, 201, 201] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 29, 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, 33, 34, 35, 36, 37]) total number of confs: 816 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: REAL250005051916 none CC(CNC(=O)CC1CC1C)NC(=O)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: [10, 4, 10, 29, 69, 69, 69, 174, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 29, 29, 69, 174, 173, 201, 201, 201, 201, 201, 201, 201, 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: 772 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051916 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051916 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051916/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051916 Building REAL250005051917 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051917' /scratch/stefan/7921156/working/building/REAL250005051917 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051917 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051917/0 /scratch/stefan/7921156/working/building/REAL250005051917 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/25 `/scratch/stefan/7921156/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(CC)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051917.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051917 none C=CC(C)(CC)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 169, 96, 169, 169, 189, 96, 96, 40, 15, 6, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 198, 198, 198, 169, 169, 169, 201, 201, 201, 201, 201, 96, 40, 40, 15, 15, 15, 15, 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: 1026 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051917 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051917 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051917/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051917 Building REAL250005051918 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051918' /scratch/stefan/7921156/working/building/REAL250005051918 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051918 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051918/0 /scratch/stefan/7921156/working/building/REAL250005051918 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/26 `/scratch/stefan/7921156/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C[C@H]1CCOC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051918.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051918 none CC(CNC(=O)C[C@H]1CCOC1)NC(=O)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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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, 7] 0 hydrogens 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, 119, 38, 38, 9, 38, 1, 1, 1, 1, 1, 1, 1, 177, 201, 201, 201, 201, 201, 201, 201, 201, 177, 177, 177, 177, 119, 119, 38, 9, 9, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38]) total number of confs: 816 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: REAL250005051918 none CC(CNC(=O)C[C@H]1CCOC1)NC(=O)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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 12, 34, 81, 81, 81, 173, 201, 201, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 34, 34, 81, 173, 173, 201, 201, 201, 201, 201, 201, 4, 1] 201 rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 779 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051918 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051918 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051918/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051918 Building REAL250005051919 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051919' /scratch/stefan/7921156/working/building/REAL250005051919 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051919 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051919/0 /scratch/stefan/7921156/working/building/REAL250005051919 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/27 `/scratch/stefan/7921156/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005051919.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051919 none CCC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 119, 121, 166, 166, 166, 175, 175, 175, 175, 175, 1, 1, 3, 3, 3, 3, 3, 7, 42, 42, 121, 121, 121, 121, 166, 175, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 36, 37, 35, 34, 18, 19] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 679 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: REAL250005051919 none CCC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 78, 78, 78, 45, 19, 7, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 175, 175, 201, 201, 201, 201, 201, 78, 45, 45, 19, 19, 19, 19, 7, 1, 175, 175, 175, 175] 201 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 712 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051919 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051919 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051919/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051919 Building REAL250005051920 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051920' /scratch/stefan/7921156/working/building/REAL250005051920 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051920 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051920/0 /scratch/stefan/7921156/working/building/REAL250005051920 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/28 `/scratch/stefan/7921156/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC(C)(F)F)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051920.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051920 none CC(CNC(=O)CC(C)(F)F)NC(=O)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', 'F', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 26, 71, 71, 71, 179, 189, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 26, 26, 71, 179, 179, 201, 201, 201, 4, 1] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 897 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051920 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051920 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051920/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051920 Building REAL250005051921 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051921' /scratch/stefan/7921156/working/building/REAL250005051921 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051921 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051921/0 /scratch/stefan/7921156/working/building/REAL250005051921 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/29 `/scratch/stefan/7921156/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005051921.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051921 none CCCC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 1, 1, 1, 7, 7, 7, 33, 87, 87, 137, 137, 137, 146, 146, 146, 146, 146, 1, 1, 8, 8, 8, 8, 8, 6, 6, 7, 33, 33, 87, 87, 87, 87, 137, 146, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 37, 38, 39, 40, 19, 20] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 582 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: REAL250005051921 none CCCC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 178, 146, 66, 66, 66, 29, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 146, 146, 201, 201, 201, 201, 201, 178, 178, 66, 29, 29, 12, 12, 12, 12, 4, 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: 804 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051921 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051921 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051921/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051921 Building REAL250005051922 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051922' /scratch/stefan/7921156/working/building/REAL250005051922 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051922 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051922/0 /scratch/stefan/7921156/working/building/REAL250005051922 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/30 `/scratch/stefan/7921156/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H]1C[C@H]1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051922.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051922 none CCC[C@@H]1C[C@H]1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 54, 101, 101, 132, 132, 132, 137, 137, 137, 137, 137, 13, 13, 13, 13, 13, 7, 7, 1, 1, 11, 54, 54, 101, 101, 101, 101, 132, 137] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 608 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051922 none CCC[C@@H]1C[C@H]1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 137, 137, 137, 137, 45, 137, 45, 45, 19, 8, 3, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 194, 194, 137, 137, 45, 19, 19, 8, 8, 8, 8, 3, 1] 201 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 759 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051922 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051922 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051922/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051922 Building REAL250005051923 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051923' /scratch/stefan/7921156/working/building/REAL250005051923 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051923 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051923/0 /scratch/stefan/7921156/working/building/REAL250005051923 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/31 `/scratch/stefan/7921156/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005051923.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051923 none CC(C)C1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 1, 1, 7, 7, 7, 38, 111, 114, 178, 178, 178, 191, 191, 191, 191, 191, 1, 1, 9, 9, 9, 9, 9, 9, 9, 7, 38, 38, 114, 114, 114, 114, 178, 191, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 37, 38, 39, 40, 19, 20] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 741 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: REAL250005051923 none CC(C)C1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 201, 114, 114, 114, 54, 21, 9, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 191, 191, 201, 201, 201, 201, 201, 201, 201, 114, 54, 54, 21, 21, 21, 21, 9, 1, 191, 191, 191, 191] 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: 687 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051923 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051923 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051923/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051923 Building REAL250005051924 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051924' /scratch/stefan/7921156/working/building/REAL250005051924 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051924 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051924/0 /scratch/stefan/7921156/working/building/REAL250005051924 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/32 `/scratch/stefan/7921156/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C)(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005051924.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051924 none C=C1CC(C)(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 40, 115, 117, 155, 155, 155, 165, 165, 165, 165, 165, 1, 1, 1, 1, 1, 2, 2, 2, 6, 40, 40, 117, 117, 117, 117, 155, 165, 1, 1] 165 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 23, 24, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 645 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: REAL250005051924 none C=C1CC(C)(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 92, 165, 92, 92, 49, 18, 9, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 165, 165, 165, 92, 49, 49, 18, 18, 18, 18, 9, 1, 165, 165] 165 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: 521 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051924 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051924 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051924/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051924 Building REAL250005051925 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051925' /scratch/stefan/7921156/working/building/REAL250005051925 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051925 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051925/0 /scratch/stefan/7921156/working/building/REAL250005051925 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/33 `/scratch/stefan/7921156/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(CF)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051925.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051925 none CC(CNC(=O)C1(CF)CC1)NC(=O)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.2', 'O.2', 'C.2', 'C.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, 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: [112, 38, 7, 7, 1, 7, 1, 1, 9, 1, 1, 112, 182, 182, 182, 189, 189, 189, 189, 189, 112, 112, 112, 112, 38, 38, 7, 9, 9, 1, 1, 1, 1, 182, 189] 201 rigid atoms, others: [32, 4, 6, 7, 9, 10, 29, 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, 33, 34]) total number of confs: 729 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: REAL250005051925 none CC(CNC(=O)C1(CF)CC1)NC(=O)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.2', 'O.2', 'C.2', 'C.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, 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: [12, 4, 12, 40, 98, 98, 98, 189, 201, 189, 189, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 40, 40, 98, 201, 201, 189, 189, 189, 189, 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: 664 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051925 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051925 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051925/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051925 Building REAL250005051926 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051926' /scratch/stefan/7921156/working/building/REAL250005051926 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051926 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051926/0 /scratch/stefan/7921156/working/building/REAL250005051926 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/34 `/scratch/stefan/7921156/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC2(CC2)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051926.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051926 none CC(CNC(=O)C1CC2(CC2)C1)NC(=O)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, 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: [137, 61, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 138, 194, 194, 194, 201, 201, 201, 201, 201, 138, 138, 138, 138, 61, 61, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 194, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 36, 28, 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, 37, 38]) total number of confs: 778 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: REAL250005051926 none CC(CNC(=O)C1CC2(CC2)C1)NC(=O)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, 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: [19, 8, 19, 57, 118, 118, 118, 201, 201, 201, 201, 201, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 57, 57, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 8, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 679 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051926 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051926 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051926/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051926 Building REAL250005051927 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051927' /scratch/stefan/7921156/working/building/REAL250005051927 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051927 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051927/0 /scratch/stefan/7921156/working/building/REAL250005051927 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/35 `/scratch/stefan/7921156/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051927.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051927 none CC(CNC(=O)C(C)(C)C)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 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, 4, 7, 6, 7, 7, 7, 3, 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: [19, 9, 19, 43, 62, 62, 62, 68, 68, 68, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 43, 43, 62, 68, 68, 68, 68, 68, 68, 68, 68, 68, 9, 1] 68 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: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051927 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051927 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051927/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051927 Building REAL250005051928 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051928' /scratch/stefan/7921156/working/building/REAL250005051928 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051928 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051928/0 /scratch/stefan/7921156/working/building/REAL250005051928 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/36 `/scratch/stefan/7921156/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051928.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051928 none CCCCCCC(=O)NCC(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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 199, 187, 171, 141, 54, 54, 54, 25, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 195, 201, 201, 201, 201, 201, 201, 187, 187, 173, 173, 141, 141, 54, 25, 25, 9, 9, 9, 9, 4, 1] 201 rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 923 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051928 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051928 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051928/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051928 Building REAL250005051929 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051929' /scratch/stefan/7921156/working/building/REAL250005051929 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005051929 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051929/0 /scratch/stefan/7921156/working/building/REAL250005051929 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/37 `/scratch/stefan/7921156/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051929.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051929 none CC[N@H+](C)CCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 18, 28, 28, 18, 12, 12, 12, 10, 5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 12, 10, 10, 5, 5, 5, 5, 3, 1] 28 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: 132 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051929 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005051929/1 /scratch/stefan/7921156/working/building/REAL250005051929 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/38 `/scratch/stefan/7921156/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051929.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005051929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051929/1/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: REAL250005051929 none CC[N@@H+](C)CCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 24, 30, 30, 24, 14, 14, 14, 10, 6, 4, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 24, 24, 24, 24, 14, 10, 10, 6, 6, 6, 6, 4, 1] 30 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: 134 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051929 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051929 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051929/0.* 1: /scratch/stefan/7921156/working/building/REAL250005051929/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051929 Building REAL250005051930 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051930' /scratch/stefan/7921156/working/building/REAL250005051930 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051930 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051930/0 /scratch/stefan/7921156/working/building/REAL250005051930 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/39 `/scratch/stefan/7921156/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CON=C1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051930.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051930 none CC1=CON=C1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 67, 69, 103, 103, 103, 113, 113, 113, 113, 113, 2, 2, 2, 1, 5, 23, 23, 69, 69, 69, 69, 103, 113] 113 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 404 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: REAL250005051930 none CC1=CON=C1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 111, 111, 111, 62, 26, 9, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 111, 62, 62, 26, 26, 26, 26, 9, 1] 113 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 402 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051930 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051930 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051930/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051930 Building REAL250005051931 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051931' /scratch/stefan/7921156/working/building/REAL250005051931 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051931 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051931/0 /scratch/stefan/7921156/working/building/REAL250005051931 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/40 `/scratch/stefan/7921156/working/3D/40' -> `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)=O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051931.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051931 none CC(CNC(=O)[C@H]1C[C@H]1C(N)=O)NC(=O)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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [118, 49, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 8, 8, 119, 166, 166, 166, 175, 175, 175, 175, 175, 119, 119, 119, 119, 49, 49, 9, 1, 1, 8, 8, 166, 175] 196 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]) total number of confs: 675 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: REAL250005051931 none CC(CNC(=O)[C@H]1C[C@H]1C(N)=O)NC(=O)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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 19, 49, 103, 103, 103, 175, 175, 175, 175, 175, 196, 196, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 49, 49, 103, 175, 175, 196, 196, 7, 1] 196 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: 654 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051931 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051931 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051931/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051931 Building REAL250005051932 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051932' /scratch/stefan/7921156/working/building/REAL250005051932 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051932 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051932/0 /scratch/stefan/7921156/working/building/REAL250005051932 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/41 `/scratch/stefan/7921156/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005051932.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051932 none CC[C@@H](C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 30, 30, 30, 30, 22, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 30, 33, 33, 33, 34, 34, 34, 34, 34, 30, 22, 22, 10, 10, 10, 10, 4, 1, 33, 33, 33, 33, 33, 33] 36 rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051932 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051932 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051932/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051932 Building REAL250005051933 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051933' /scratch/stefan/7921156/working/building/REAL250005051933 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051933 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051933/0 /scratch/stefan/7921156/working/building/REAL250005051933 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/42 `/scratch/stefan/7921156/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(CF)CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051933.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051933 none CC(CNC(=O)C1(CF)CCC1)NC(=O)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, 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: [112, 40, 6, 6, 1, 6, 1, 1, 8, 1, 1, 1, 112, 175, 175, 175, 185, 185, 185, 185, 185, 112, 112, 112, 112, 40, 40, 6, 8, 8, 1, 1, 1, 1, 1, 1, 175, 185] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 5, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37]) total number of confs: 727 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: REAL250005051933 none CC(CNC(=O)C1(CF)CCC1)NC(=O)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, 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: [12, 4, 12, 35, 82, 82, 82, 185, 201, 185, 185, 185, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 35, 35, 82, 201, 201, 185, 185, 185, 185, 185, 185, 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: 667 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051933 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051933 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051933/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051933 Building REAL250005051934 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051934' /scratch/stefan/7921156/working/building/REAL250005051934 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051934 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051934/0 /scratch/stefan/7921156/working/building/REAL250005051934 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/43 `/scratch/stefan/7921156/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN1C=NC=N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051934.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051934 none CC(CNC(=O)CN1C=NC=N1)NC(=O)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.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 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, 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: [180, 133, 41, 41, 8, 41, 1, 1, 1, 1, 1, 1, 180, 201, 201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 180, 133, 133, 41, 8, 8, 1, 1, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 30, 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, 32, 33]) total number of confs: 810 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051934 none CC(CNC(=O)CN1C=NC=N1)NC(=O)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.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 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, 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: [10, 4, 10, 25, 74, 74, 74, 165, 201, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 25, 25, 74, 165, 165, 201, 201, 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: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051934 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051934 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051934/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051934 Building REAL250005051935 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051935' /scratch/stefan/7921156/working/building/REAL250005051935 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005051935 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051935/0 /scratch/stefan/7921156/working/building/REAL250005051935 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/44 `/scratch/stefan/7921156/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1=NNC=N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051935.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051935 none CC(CNC(=O)CC1=NNC=N1)NC(=O)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', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [165, 127, 45, 45, 9, 45, 1, 1, 1, 1, 1, 1, 165, 184, 184, 184, 184, 184, 184, 184, 184, 165, 165, 165, 165, 127, 127, 45, 9, 9, 1, 1, 184, 184] 184 rigid atoms, others: [6, 7, 8, 9, 10, 11, 30, 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, 32, 33]) total number of confs: 753 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: REAL250005051935 none CC(CNC(=O)CC1=NNC=N1)NC(=O)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', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 12, 32, 74, 74, 74, 138, 184, 184, 184, 184, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 32, 32, 74, 138, 138, 184, 184, 5, 1] 184 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: 610 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051935 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005051935/1 /scratch/stefan/7921156/working/building/REAL250005051935 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/45 `/scratch/stefan/7921156/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1=NN=CN1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051935.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005051935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051935/1/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: REAL250005051935 none CC(CNC(=O)CC1=NN=CN1)NC(=O)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', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.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, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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] 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: [148, 103, 35, 35, 6, 35, 1, 1, 1, 1, 1, 1, 148, 168, 168, 168, 170, 170, 170, 170, 170, 148, 148, 148, 148, 103, 103, 35, 6, 6, 1, 1, 168, 170] 170 rigid atoms, others: [6, 7, 8, 9, 10, 11, 30, 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, 32, 33]) total number of confs: 699 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: REAL250005051935 none CC(CNC(=O)CC1=NN=CN1)NC(=O)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', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.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, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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] 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: [13, 7, 13, 32, 89, 89, 89, 159, 170, 170, 170, 170, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 32, 32, 89, 159, 159, 170, 170, 7, 1] 170 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 622 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051935 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051935 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051935/0.* 1: /scratch/stefan/7921156/working/building/REAL250005051935/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051935 Building REAL250005051936 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051936' /scratch/stefan/7921156/working/building/REAL250005051936 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051936 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051936/0 /scratch/stefan/7921156/working/building/REAL250005051936 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/46 `/scratch/stefan/7921156/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051936.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051936 none CC(C)C(C)C(=O)NCC(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 175, 183, 107, 175, 107, 107, 53, 20, 8, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 183, 183, 183, 183, 183, 183, 183, 175, 175, 175, 175, 107, 53, 53, 20, 20, 20, 20, 8, 1] 183 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: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051936 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051936 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051936/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051936 Building REAL250005051937 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051937' /scratch/stefan/7921156/working/building/REAL250005051937 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051937 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051937/0 /scratch/stefan/7921156/working/building/REAL250005051937 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/47 `/scratch/stefan/7921156/working/3D/47' -> `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)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051937.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051937 none CC[C@@H]1C[C@H]1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 128, 128, 175, 175, 175, 177, 177, 177, 177, 177, 3, 3, 3, 3, 3, 1, 1, 12, 61, 61, 128, 128, 128, 128, 175, 177] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 707 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: REAL250005051937 none CC[C@@H]1C[C@H]1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 177, 177, 177, 177, 78, 177, 78, 78, 34, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 177, 177, 78, 34, 34, 12, 12, 12, 12, 4, 1] 201 rigid atoms, others: [37, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 690 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051937 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051937 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051937/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051937 Building REAL250005051938 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051938' /scratch/stefan/7921156/working/building/REAL250005051938 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051938 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051938/0 /scratch/stefan/7921156/working/building/REAL250005051938 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/48 `/scratch/stefan/7921156/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051938.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051938 none CC(C)CCCC(=O)NCC(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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 176, 158, 156, 61, 61, 61, 23, 8, 4, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 198, 201, 201, 201, 201, 197, 194, 183, 183, 156, 156, 61, 23, 23, 8, 8, 8, 8, 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: 1175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051938 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051938 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051938/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051938 Building REAL250005051939 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051939' /scratch/stefan/7921156/working/building/REAL250005051939 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051939 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051939/0 /scratch/stefan/7921156/working/building/REAL250005051939 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/49 `/scratch/stefan/7921156/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC12CC2)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051939.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051939 none CC(CNC(=O)C1CC12CC2)NC(=O)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'] 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 65, 13, 13, 1, 13, 1, 1, 1, 1, 1, 147, 196, 196, 196, 201, 201, 201, 201, 201, 147, 147, 147, 147, 65, 65, 13, 1, 1, 1, 1, 1, 1, 1, 196, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 27, 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, 34, 35]) total number of confs: 797 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: REAL250005051939 none CC(CNC(=O)C1CC12CC2)NC(=O)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'] 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 19, 58, 112, 112, 112, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 58, 58, 112, 201, 201, 201, 201, 201, 201, 201, 7, 1] 201 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 663 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051939 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051939 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051939/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051939 Building REAL250005051940 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051940' /scratch/stefan/7921156/working/building/REAL250005051940 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005051940 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051940/0 /scratch/stefan/7921156/working/building/REAL250005051940 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/50 `/scratch/stefan/7921156/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1=CNC=N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051940.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051940 none CC(CNC(=O)CC1=CNC=N1)NC(=O)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', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [164, 114, 35, 35, 8, 35, 1, 1, 1, 1, 1, 1, 164, 184, 184, 184, 185, 185, 185, 185, 185, 164, 164, 164, 164, 114, 114, 35, 8, 8, 1, 1, 1, 184, 185] 185 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 30, 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, 33, 34]) 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: REAL250005051940 none CC(CNC(=O)CC1=CNC=N1)NC(=O)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', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 5, 12, 30, 67, 67, 67, 147, 185, 185, 185, 185, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 30, 30, 67, 147, 147, 185, 185, 185, 5, 1] 185 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 637 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051940 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005051940/1 /scratch/stefan/7921156/working/building/REAL250005051940 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/51 `/scratch/stefan/7921156/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1=CN=CN1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051940.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005051940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051940/1/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: REAL250005051940 none CC(CNC(=O)CC1=CN=CN1)NC(=O)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', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 8, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 116, 33, 33, 5, 33, 1, 1, 1, 1, 1, 1, 180, 200, 200, 200, 201, 201, 201, 201, 201, 180, 180, 180, 180, 116, 116, 33, 5, 5, 1, 1, 1, 200, 201] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 30, 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, 33, 34]) total number of confs: 840 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: REAL250005051940 none CC(CNC(=O)CC1=CN=CN1)NC(=O)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', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 8, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 12, 29, 73, 73, 73, 163, 201, 201, 201, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 29, 29, 73, 163, 163, 201, 201, 201, 6, 1] 201 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 679 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051940 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051940 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051940/0.* 1: /scratch/stefan/7921156/working/building/REAL250005051940/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051940 Building REAL250005051941 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051941' /scratch/stefan/7921156/working/building/REAL250005051941 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051941 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051941/0 /scratch/stefan/7921156/working/building/REAL250005051941 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/52 `/scratch/stefan/7921156/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1CC(=O)N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051941.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051941 none CC(CNC(=O)[C@@H]1CC(=O)N1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [116, 61, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 116, 129, 129, 129, 133, 133, 133, 133, 133, 116, 116, 116, 116, 61, 61, 12, 1, 1, 1, 129, 133] 133 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32]) total number of confs: 539 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: REAL250005051941 none CC(CNC(=O)[C@@H]1CC(=O)N1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 41, 87, 87, 87, 133, 133, 133, 133, 133, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 41, 41, 87, 133, 133, 133, 9, 1] 133 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: 454 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051941 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051941 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051941/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051941 Building REAL250005051942 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051942' /scratch/stefan/7921156/working/building/REAL250005051942 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051942 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051942/0 /scratch/stefan/7921156/working/building/REAL250005051942 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/53 `/scratch/stefan/7921156/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCCCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051942.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051942 none CC(CNC(=O)C1=CCCCC1)NC(=O)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 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [126, 59, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 127, 165, 165, 165, 170, 170, 170, 170, 170, 127, 127, 127, 127, 59, 59, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 165, 170] 170 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 36, 28, 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, 37, 38]) total number of confs: 666 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: REAL250005051942 none CC(CNC(=O)C1=CCCCC1)NC(=O)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 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [25, 9, 25, 63, 128, 128, 128, 170, 170, 170, 170, 170, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 63, 63, 128, 170, 170, 170, 170, 170, 170, 170, 170, 170, 9, 1] 170 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: 514 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051942 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051942 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051942/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051942 Building REAL250005051943 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051943' /scratch/stefan/7921156/working/building/REAL250005051943 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051943 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051943/0 /scratch/stefan/7921156/working/building/REAL250005051943 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/54 `/scratch/stefan/7921156/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005051943.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051943 none CC(=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [194, 194, 110, 110, 110, 46, 16, 5, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 194, 201, 201, 194, 194, 194, 194, 110, 46, 46, 16, 16, 16, 16, 5, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 677 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051943 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051943 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051943/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051943 Building REAL250005051944 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051944' /scratch/stefan/7921156/working/building/REAL250005051944 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051944 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051944/0 /scratch/stefan/7921156/working/building/REAL250005051944 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/55 `/scratch/stefan/7921156/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H]1CC(=O)N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051944.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051944 none CC(CNC(=O)[C@H]1CC(=O)N1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [142, 67, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 142, 176, 176, 176, 186, 186, 186, 186, 186, 142, 142, 142, 142, 67, 67, 13, 1, 1, 1, 176, 186] 186 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32]) total number of confs: 727 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: REAL250005051944 none CC(CNC(=O)[C@H]1CC(=O)N1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [21, 9, 21, 59, 123, 123, 123, 186, 186, 186, 186, 186, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 59, 59, 123, 186, 186, 186, 10, 1] 186 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: 637 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051944 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051944 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051944/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051944 Building REAL250005051945 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051945' /scratch/stefan/7921156/working/building/REAL250005051945 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051945 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051945/0 /scratch/stefan/7921156/working/building/REAL250005051945 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/56 `/scratch/stefan/7921156/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN1C=NC=N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051945.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051945 none CC(CNC(=O)CN1C=NC=N1)NC(=O)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.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 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, 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: [180, 133, 41, 41, 8, 41, 1, 1, 1, 1, 1, 1, 180, 201, 201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 180, 133, 133, 41, 8, 8, 1, 1, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 30, 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, 32, 33]) total number of confs: 810 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051945 none CC(CNC(=O)CN1C=NC=N1)NC(=O)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.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 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, 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: [10, 4, 10, 25, 74, 74, 74, 165, 201, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 25, 25, 74, 165, 165, 201, 201, 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: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051945 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051945 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051945/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051945 Building REAL250005051946 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051946' /scratch/stefan/7921156/working/building/REAL250005051946 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051946 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051946/0 /scratch/stefan/7921156/working/building/REAL250005051946 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/57 `/scratch/stefan/7921156/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005051946.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051946 none COC1(C(=O)NCC(C)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 10, 10, 10, 52, 132, 133, 167, 167, 167, 184, 184, 184, 184, 184, 1, 1, 6, 6, 6, 10, 52, 52, 133, 133, 133, 133, 167, 184, 1, 1, 1, 1] 184 rigid atoms, others: [32, 1, 2, 3, 35, 33, 34, 18, 19] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 695 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: REAL250005051946 none COC1(C(=O)NCC(C)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 135, 135, 135, 63, 20, 9, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 135, 63, 63, 20, 20, 20, 20, 9, 1, 184, 184, 184, 184] 184 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: 617 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051946 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051946 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051946/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051946 Building REAL250005051947 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051947' /scratch/stefan/7921156/working/building/REAL250005051947 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051947 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051947/0 /scratch/stefan/7921156/working/building/REAL250005051947 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/58 `/scratch/stefan/7921156/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CSC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051947.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051947 none CC(CNC(=O)C1CSC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 14, 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, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [126, 55, 12, 12, 1, 12, 1, 1, 1, 1, 127, 167, 167, 167, 172, 172, 172, 172, 172, 127, 127, 127, 127, 55, 55, 12, 1, 1, 1, 1, 1, 167, 172] 172 rigid atoms, others: [4, 6, 7, 8, 9, 26, 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, 31, 32]) total number of confs: 672 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: REAL250005051947 none CC(CNC(=O)C1CSC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 14, 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, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [24, 10, 24, 62, 125, 125, 125, 172, 172, 172, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 62, 62, 125, 172, 172, 172, 172, 172, 10, 1] 172 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: 592 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051947 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051947 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051947/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051947 Building REAL250005051948 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051948' /scratch/stefan/7921156/working/building/REAL250005051948 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051948 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051948/0 /scratch/stefan/7921156/working/building/REAL250005051948 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/59 `/scratch/stefan/7921156/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(O)CCCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051948.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051948 none CC(CNC(=O)C1(O)CCCC1)NC(=O)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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [103, 52, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 103, 131, 131, 131, 134, 134, 134, 134, 134, 103, 103, 103, 103, 52, 52, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 131, 134] 402 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 36, 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, 37, 38]) total number of confs: 535 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051948 none CC(CNC(=O)C1(O)CCCC1)NC(=O)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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [22, 9, 22, 46, 101, 101, 101, 134, 134, 134, 134, 134, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 46, 46, 101, 402, 134, 134, 134, 134, 134, 134, 134, 134, 9, 1] 402 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: 851 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051948 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051948 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051948/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051948 Building REAL250005051949 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051949' /scratch/stefan/7921156/working/building/REAL250005051949 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051949 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051949/0 /scratch/stefan/7921156/working/building/REAL250005051949 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/60 `/scratch/stefan/7921156/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051949.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051949 none C=CCC(=O)NCC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 193, 132, 132, 132, 66, 23, 10, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 195, 195, 195, 193, 193, 132, 66, 66, 23, 23, 23, 23, 10, 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: 778 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051949 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051949 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051949/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051949 Building REAL250005051950 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051950' /scratch/stefan/7921156/working/building/REAL250005051950 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005051950 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051950/0 /scratch/stefan/7921156/working/building/REAL250005051950 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/61 `/scratch/stefan/7921156/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C[NH+](C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051950.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051950 none CC(CNC(=O)C[NH+](C)C)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.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, 9, 6, 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, 1, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 8, 9, 11, 11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 1] 11 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: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051950 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005051950/1 /scratch/stefan/7921156/working/building/REAL250005051950 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/62 `/scratch/stefan/7921156/working/3D/62' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051950.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005051950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051950/1/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: REAL250005051950 none CC(CNC(=O)CN(C)C)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.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, 10, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [16, 6, 16, 41, 99, 99, 99, 191, 201, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 41, 41, 99, 191, 191, 201, 201, 201, 201, 201, 201, 6, 1] 201 rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 787 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051950 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051950 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051950/0.* 1: /scratch/stefan/7921156/working/building/REAL250005051950/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051950 Building REAL250005051951 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051951' /scratch/stefan/7921156/working/building/REAL250005051951 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051951 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051951/0 /scratch/stefan/7921156/working/building/REAL250005051951 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/63 `/scratch/stefan/7921156/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051951.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051951 none C=CC(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 582 conformations in input total number of sets (complete confs): 582 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 141, 194, 141, 141, 65, 22, 9, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 582, 141, 65, 65, 22, 22, 22, 22, 9, 1] 582 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: 1318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051951 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051951 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051951/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051951 Building REAL250005051952 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051952' /scratch/stefan/7921156/working/building/REAL250005051952 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051952 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051952/0 /scratch/stefan/7921156/working/building/REAL250005051952 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/64 `/scratch/stefan/7921156/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCCN=[N+]=[N-])NC(=O)C1=CC(=O)[N-]O1) `REAL250005051952.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051952 none CC(CNC(=O)CCCN=[N+]=[N-])NC(=O)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.2', 'N.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 8, 8, 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: [5, 3, 5, 9, 22, 22, 22, 76, 75, 150, 201, 201, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 22, 76, 76, 99, 99, 136, 138, 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: 854 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051952 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051952 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051952/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051952 Building REAL250005051953 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051953' /scratch/stefan/7921156/working/building/REAL250005051953 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051953 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051953/0 /scratch/stefan/7921156/working/building/REAL250005051953 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/65 `/scratch/stefan/7921156/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1OCC1(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051953.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051953 none CC(CNC(=O)C1OCC1(C)C)NC(=O)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 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [66, 33, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 66, 89, 89, 89, 92, 92, 92, 92, 92, 66, 66, 66, 66, 33, 33, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 89, 92] 92 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 366 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: REAL250005051953 none CC(CNC(=O)C1OCC1(C)C)NC(=O)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 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 19, 41, 78, 78, 78, 92, 92, 92, 92, 92, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 41, 41, 78, 92, 92, 92, 92, 92, 92, 92, 92, 92, 9, 1] 92 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: 327 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051953 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051953 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051953/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051953 Building REAL250005051954 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051954' /scratch/stefan/7921156/working/building/REAL250005051954 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005051954 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051954/0 /scratch/stefan/7921156/working/building/REAL250005051954 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/66 `/scratch/stefan/7921156/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)N1CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051954.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051954 none CC(CNC(=O)C(C)N1CCC1)NC(=O)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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [164, 92, 22, 22, 4, 22, 1, 4, 1, 1, 1, 1, 164, 190, 190, 190, 195, 195, 195, 195, 195, 164, 164, 164, 164, 92, 92, 22, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 190, 195] 195 rigid atoms, others: [32, 33, 34, 35, 36, 37, 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, 38, 39]) total number of confs: 788 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: REAL250005051954 none CC(CNC(=O)C(C)N1CCC1)NC(=O)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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 22, 52, 125, 125, 125, 195, 195, 195, 195, 195, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 52, 52, 125, 195, 195, 195, 195, 195, 195, 195, 195, 195, 195, 10, 1] 195 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: 744 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051954 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005051954/1 /scratch/stefan/7921156/working/building/REAL250005051954 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/67 `/scratch/stefan/7921156/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)[NH+]1CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051954.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005051954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051954/1/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: REAL250005051954 none CC(CNC(=O)C(C)[NH+]1CCC1)NC(=O)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.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, 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, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [17, 14, 11, 11, 4, 11, 1, 4, 1, 1, 1, 1, 1, 17, 17, 17, 17, 20, 20, 20, 20, 20, 17, 17, 17, 17, 14, 14, 11, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 17, 20] 20 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40]) 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: REAL250005051954 none CC(CNC(=O)C(C)[NH+]1CCC1)NC(=O)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.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, 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, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 11, 14, 19, 19, 19, 20, 20, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 14, 14, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 1] 20 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: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051954 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051954 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051954/0.* 1: /scratch/stefan/7921156/working/building/REAL250005051954/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051954 Building REAL250005051955 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051955' /scratch/stefan/7921156/working/building/REAL250005051955 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051955 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051955/0 /scratch/stefan/7921156/working/building/REAL250005051955 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/68 `/scratch/stefan/7921156/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H]1CC1(F)F)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051955.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051955 none CC(CNC(=O)[C@H]1CC1(F)F)NC(=O)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', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 75, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 161, 193, 193, 193, 201, 201, 201, 201, 201, 161, 161, 161, 161, 75, 75, 13, 1, 1, 193, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 797 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: REAL250005051955 none CC(CNC(=O)[C@H]1CC1(F)F)NC(=O)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', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 8, 22, 58, 125, 125, 125, 201, 201, 201, 201, 201, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 58, 58, 125, 201, 201, 8, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 659 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051955 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051955 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051955/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051955 Building REAL250005051956 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051956' /scratch/stefan/7921156/working/building/REAL250005051956 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051956 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051956/0 /scratch/stefan/7921156/working/building/REAL250005051956 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/69 `/scratch/stefan/7921156/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1=CNN=C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051956.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051956 none CC(CNC(=O)CC1=CNN=C1)NC(=O)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', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 86, 22, 22, 8, 22, 1, 1, 1, 1, 1, 1, 157, 198, 198, 198, 201, 201, 201, 201, 201, 157, 157, 157, 157, 86, 86, 22, 8, 8, 1, 1, 1, 198, 201] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 30, 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, 33, 34]) total number of confs: 813 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: REAL250005051956 none CC(CNC(=O)CC1=CNN=C1)NC(=O)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', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 18, 44, 106, 106, 106, 192, 197, 197, 197, 197, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 44, 44, 106, 192, 192, 197, 197, 197, 8, 1] 197 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: 757 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051956 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051956 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051956/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051956 Building REAL250005051957 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051957' /scratch/stefan/7921156/working/building/REAL250005051957 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051957 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051957/0 /scratch/stefan/7921156/working/building/REAL250005051957 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/70 `/scratch/stefan/7921156/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051957.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051957 none CC(C)NC(=O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 197, 200, 197, 159, 199, 159, 159, 67, 22, 9, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 200, 200, 199, 200, 200, 200, 200, 199, 159, 67, 67, 22, 22, 22, 22, 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: 696 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051957 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051957 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051957/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051957 Building REAL250005051958 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051958' /scratch/stefan/7921156/working/building/REAL250005051958 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051958 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051958/0 /scratch/stefan/7921156/working/building/REAL250005051958 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/71 `/scratch/stefan/7921156/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005051958.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051958 none CC1=C(C(=O)NCC(C)NC(=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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 51, 119, 121, 157, 157, 157, 169, 169, 169, 169, 169, 1, 1, 1, 2, 2, 2, 9, 51, 51, 121, 121, 121, 121, 157, 169, 1, 1, 1, 1] 169 rigid atoms, others: [0, 1, 2, 3, 36, 35, 33, 34, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 654 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: REAL250005051958 none CC1=C(C(=O)NCC(C)NC(=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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 112, 112, 112, 55, 22, 9, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 169, 169, 112, 55, 55, 22, 22, 22, 22, 9, 1, 169, 169, 169, 169] 169 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: 479 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051958 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051958 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051958/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051958 Building REAL250005051959 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051959' /scratch/stefan/7921156/working/building/REAL250005051959 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051959 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051959/0 /scratch/stefan/7921156/working/building/REAL250005051959 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/72 `/scratch/stefan/7921156/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=C1CCCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051959.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051959 none CC(CNC(=O)C=C1CCCC1)NC(=O)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: [149, 56, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 149, 197, 197, 197, 201, 201, 201, 201, 201, 149, 149, 149, 149, 56, 56, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 197, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 36, 28, 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, 37, 38]) total number of confs: 785 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: REAL250005051959 none CC(CNC(=O)C=C1CCCC1)NC(=O)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: [19, 7, 19, 57, 124, 124, 124, 201, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 57, 57, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 7, 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: 669 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051959 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051959 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051959/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051959 Building REAL250005051960 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051960' /scratch/stefan/7921156/working/building/REAL250005051960 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005051960 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051960/0 /scratch/stefan/7921156/working/building/REAL250005051960 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/73 `/scratch/stefan/7921156/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C[N@H+](C)C1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051960.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051960 none CC(CNC(=O)C[N@H+](C)C1CC1)NC(=O)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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 10, 10, 6, 10, 3, 1, 3, 3, 1, 1, 1, 16, 16, 16, 16, 17, 17, 17, 17, 17, 16, 16, 16, 16, 13, 13, 10, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 16, 17] 17 rigid atoms, others: [34, 35, 36, 37, 38, 7, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051960 none CC(CNC(=O)C[N@H+](C)C1CC1)NC(=O)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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 11, 15, 15, 15, 17, 17, 17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 11, 11, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 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: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051960 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005051960/1 /scratch/stefan/7921156/working/building/REAL250005051960 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/74 `/scratch/stefan/7921156/working/3D/74' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C[N@@H+](C)C1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051960.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005051960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051960/1/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: REAL250005051960 none CC(CNC(=O)C[N@@H+](C)C1CC1)NC(=O)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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 19, 14, 14, 5, 14, 2, 1, 2, 2, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 19, 19, 14, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 24, 24] 24 rigid atoms, others: [34, 35, 36, 37, 38, 7, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) 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: REAL250005051960 none CC(CNC(=O)C[N@@H+](C)C1CC1)NC(=O)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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 12, 20, 20, 20, 23, 24, 24, 24, 24, 24, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 12, 12, 20, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1] 24 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051960 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `2' /scratch/stefan/7921156/working/building/REAL250005051960/2 /scratch/stefan/7921156/working/building/REAL250005051960 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 2 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/75 `/scratch/stefan/7921156/working/3D/75' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN(C)C1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051960.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005051960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051960/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051960 none CC(CNC(=O)CN(C)C1CC1)NC(=O)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: [173, 114, 37, 37, 13, 37, 3, 1, 3, 1, 1, 1, 173, 201, 201, 201, 201, 201, 201, 201, 201, 173, 173, 173, 173, 114, 114, 37, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38, 39]) total number of confs: 846 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051960 none CC(CNC(=O)CN(C)C1CC1)NC(=O)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: [11, 4, 11, 26, 82, 82, 82, 176, 201, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 82, 176, 176, 201, 201, 201, 201, 201, 201, 201, 201, 4, 1] 201 rigid atoms, others: [39, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 750 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051960 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051960 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051960/0.* 2: /scratch/stefan/7921156/working/building/REAL250005051960/2.* 1: /scratch/stefan/7921156/working/building/REAL250005051960/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051960 Building REAL250005051961 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051961' /scratch/stefan/7921156/working/building/REAL250005051961 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051961 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051961/0 /scratch/stefan/7921156/working/building/REAL250005051961 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/76 `/scratch/stefan/7921156/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(CO)COC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051961.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051961 none CC(CNC(=O)C1(CO)COC1)NC(=O)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', '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, 5, 5, 12, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 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] 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: [105, 39, 7, 7, 1, 7, 1, 1, 8, 1, 1, 1, 105, 165, 165, 165, 178, 178, 178, 178, 178, 105, 105, 105, 105, 39, 39, 7, 8, 8, 24, 1, 1, 1, 1, 165, 178] 603 rigid atoms, others: [32, 33, 34, 4, 6, 7, 9, 10, 11, 31] set([0, 1, 2, 3, 5, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 707 number of broken/clashed sets: 294 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051961 none CC(CNC(=O)C1(CO)COC1)NC(=O)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', '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, 5, 5, 12, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 18, 40, 98, 98, 98, 178, 201, 178, 178, 178, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 40, 40, 98, 201, 201, 603, 178, 178, 178, 178, 9, 1] 603 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1308 number of broken/clashed sets: 294 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051961 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051961 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051961/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051961 Building REAL250005051962 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051962' /scratch/stefan/7921156/working/building/REAL250005051962 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051962 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051962/0 /scratch/stefan/7921156/working/building/REAL250005051962 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/77 `/scratch/stefan/7921156/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CCCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051962.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051962 none CC(C)=CCCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 185, 171, 68, 68, 68, 35, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 185, 185, 171, 171, 68, 35, 35, 11, 11, 11, 11, 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: 821 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051962 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051962 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051962/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051962 Building REAL250005051963 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051963' /scratch/stefan/7921156/working/building/REAL250005051963 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051963 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051963/0 /scratch/stefan/7921156/working/building/REAL250005051963 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/78 `/scratch/stefan/7921156/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1COC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051963.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051963 none CC(CNC(=O)C1COC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 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 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [123, 57, 12, 12, 1, 12, 1, 1, 1, 1, 124, 164, 164, 164, 170, 170, 170, 170, 170, 124, 124, 124, 124, 57, 57, 12, 1, 1, 1, 1, 1, 164, 170] 170 rigid atoms, others: [4, 6, 7, 8, 9, 26, 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, 31, 32]) total number of confs: 662 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: REAL250005051963 none CC(CNC(=O)C1COC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 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 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [25, 10, 25, 63, 115, 115, 115, 170, 170, 170, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 63, 63, 115, 170, 170, 170, 170, 170, 10, 1] 170 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: 609 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051963 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051963 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051963/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051963 Building REAL250005051964 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051964' /scratch/stefan/7921156/working/building/REAL250005051964 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051964 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051964/0 /scratch/stefan/7921156/working/building/REAL250005051964 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/79 `/scratch/stefan/7921156/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCC(C)O1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051964.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051964 none CC(CNC(=O)C1CCC(C)O1)NC(=O)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', '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, 8, 1, 11, 5, 5, 5, 5, 5, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [123, 66, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 123, 150, 150, 150, 157, 157, 157, 157, 157, 123, 123, 123, 123, 66, 66, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 150, 157] 157 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 28, 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, 34, 35, 36, 37, 38]) total number of confs: 627 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: REAL250005051964 none CC(CNC(=O)C1CCC(C)O1)NC(=O)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', '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, 8, 1, 11, 5, 5, 5, 5, 5, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 52, 103, 103, 103, 157, 157, 157, 157, 157, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 52, 52, 103, 157, 157, 157, 157, 157, 157, 157, 157, 157, 10, 1] 157 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: 524 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051964 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051964 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051964/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051964 Building REAL250005051965 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051965' /scratch/stefan/7921156/working/building/REAL250005051965 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051965 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051965/0 /scratch/stefan/7921156/working/building/REAL250005051965 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/80 `/scratch/stefan/7921156/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1(CO)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051965.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051965 none CC(CNC(=O)CC1(CO)CC1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [154, 91, 26, 26, 7, 26, 1, 1, 1, 10, 1, 1, 154, 184, 184, 184, 190, 190, 190, 190, 190, 154, 154, 154, 154, 91, 91, 26, 7, 7, 10, 10, 30, 1, 1, 1, 1, 184, 190] 603 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 10, 11] set([0, 1, 2, 3, 4, 5, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 838 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: REAL250005051965 none CC(CNC(=O)CC1(CO)CC1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 31, 72, 72, 72, 161, 190, 201, 190, 190, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 31, 31, 72, 161, 161, 201, 201, 603, 190, 190, 190, 190, 6, 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: 1405 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051965 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051965 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051965/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051965 Building REAL250005051966 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051966' /scratch/stefan/7921156/working/building/REAL250005051966 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051966 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051966/0 /scratch/stefan/7921156/working/building/REAL250005051966 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/81 `/scratch/stefan/7921156/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1C[NH+](C)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051966.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051966 none CC(CNC(=O)CC1C[NH+](C)C1)NC(=O)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.4', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 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, 1, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 10, 10, 5, 10, 1, 1, 1, 1, 1, 1, 1, 15, 16, 16, 16, 16, 16, 16, 16, 16, 15, 15, 15, 15, 13, 13, 10, 5, 5, 1, 1, 1, 2, 2, 2, 1, 1, 16, 16] 16 rigid atoms, others: [32, 33, 37, 6, 7, 8, 9, 10, 11, 12, 38, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 39, 40]) 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: REAL250005051966 none CC(CNC(=O)CC1C[NH+](C)C1)NC(=O)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.4', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 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, 1, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 1] 16 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051966 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051966 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051966/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051966 Building REAL250005051967 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051967' /scratch/stefan/7921156/working/building/REAL250005051967 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051967 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051967/0 /scratch/stefan/7921156/working/building/REAL250005051967 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/82 `/scratch/stefan/7921156/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC(C)(O)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051967.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051967 none CC(CNC(=O)C1CC(C)(O)C1)NC(=O)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'] 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [145, 69, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 146, 193, 193, 193, 201, 201, 201, 201, 201, 146, 146, 146, 146, 69, 69, 13, 1, 1, 1, 2, 2, 2, 6, 1, 1, 193, 201] 603 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 36, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 37, 38]) total number of confs: 788 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: REAL250005051967 none CC(CNC(=O)C1CC(C)(O)C1)NC(=O)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'] 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 18, 54, 123, 123, 123, 201, 201, 201, 201, 201, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 54, 54, 123, 201, 201, 201, 201, 201, 201, 603, 201, 201, 9, 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: 1259 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051967 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051967 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051967/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051967 Building REAL250005051968 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051968' /scratch/stefan/7921156/working/building/REAL250005051968 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051968 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051968/0 /scratch/stefan/7921156/working/building/REAL250005051968 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/83 `/scratch/stefan/7921156/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051968.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051968 none CO[C@H](C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 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, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 123, 149, 149, 123, 123, 66, 23, 9, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 149, 149, 123, 66, 66, 23, 23, 23, 23, 9, 1] 149 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 554 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051968 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051968 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051968/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051968 Building REAL250005051969 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051969' /scratch/stefan/7921156/working/building/REAL250005051969 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005051969 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051969/0 /scratch/stefan/7921156/working/building/REAL250005051969 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/84 `/scratch/stefan/7921156/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005051969.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051969 none CC1=NNC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 20, 58, 59, 93, 93, 93, 101, 101, 101, 101, 101, 1, 2, 2, 2, 1, 4, 20, 20, 59, 59, 59, 59, 93, 101] 101 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 365 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: REAL250005051969 none CC1=NNC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 101, 101, 101, 54, 22, 10, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 101, 54, 54, 22, 22, 22, 22, 10, 1] 101 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: 344 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051969 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005051969/1 /scratch/stefan/7921156/working/building/REAL250005051969 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/85 `/scratch/stefan/7921156/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005051969.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005051969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051969/1/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: REAL250005051969 none CC1=NN=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 64, 65, 91, 91, 91, 96, 96, 96, 96, 96, 1, 2, 2, 2, 5, 22, 22, 65, 65, 65, 65, 91, 96, 1] 96 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 20] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051969 none CC1=NN=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 96, 96, 59, 23, 10, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 59, 59, 23, 23, 23, 23, 10, 1, 96] 96 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 346 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051969 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051969 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051969/0.* 1: /scratch/stefan/7921156/working/building/REAL250005051969/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051969 Building REAL250005051970 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051970' /scratch/stefan/7921156/working/building/REAL250005051970 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005051970 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051970/0 /scratch/stefan/7921156/working/building/REAL250005051970 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/86 `/scratch/stefan/7921156/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=COC(=O)N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051970.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051970 none CC(CNC(=O)C1=COC(=O)N1)NC(=O)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', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 6, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [92, 45, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 92, 112, 112, 112, 118, 118, 118, 118, 118, 92, 92, 92, 92, 45, 45, 9, 1, 1, 112, 118] 118 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 459 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: REAL250005051970 none CC(CNC(=O)C1=COC(=O)N1)NC(=O)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', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 6, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [18, 9, 18, 47, 85, 85, 85, 118, 118, 118, 118, 118, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 47, 47, 85, 118, 118, 9, 1] 118 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 363 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051970 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005051970/1 /scratch/stefan/7921156/working/building/REAL250005051970 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/87 `/scratch/stefan/7921156/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=COC(=O)[N-]1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051970.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005051970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051970/1/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: REAL250005051970 none CC(CNC(=O)C1=COC(=O)[N-]1)NC(=O)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', 'O.2', 'N.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 5, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [37, 24, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 38, 46, 46, 46, 46, 46, 46, 46, 46, 38, 38, 38, 38, 23, 23, 8, 1, 46, 46] 46 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051970 none CC(CNC(=O)C1=COC(=O)[N-]1)NC(=O)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', 'O.2', 'N.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 5, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 22, 37, 37, 37, 46, 46, 46, 46, 46, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 22, 22, 37, 46, 5, 1] 46 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051970 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051970 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051970/0.* 1: /scratch/stefan/7921156/working/building/REAL250005051970/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051970 Building REAL250005051971 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051971' /scratch/stefan/7921156/working/building/REAL250005051971 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051971 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051971/0 /scratch/stefan/7921156/working/building/REAL250005051971 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/88 `/scratch/stefan/7921156/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051971.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051971 none CC=CC(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [170, 170, 134, 116, 134, 116, 116, 52, 21, 9, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 170, 134, 402, 116, 52, 52, 21, 21, 21, 21, 9, 1] 510 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: 1023 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051971 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051971 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051971/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051971 Building REAL250005051972 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051972' /scratch/stefan/7921156/working/building/REAL250005051972 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051972 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051972/0 /scratch/stefan/7921156/working/building/REAL250005051972 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/89 `/scratch/stefan/7921156/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051972.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051972 none CCCC[C@H](C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 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: [198, 182, 170, 120, 42, 120, 120, 42, 42, 23, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 182, 182, 174, 174, 120, 120, 120, 42, 23, 23, 10, 10, 10, 10, 4, 1] 201 rigid atoms, others: [42, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 965 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051972 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051972 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051972/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051972 Building REAL250005051973 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051973' /scratch/stefan/7921156/working/building/REAL250005051973 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005051973 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051973/0 /scratch/stefan/7921156/working/building/REAL250005051973 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/90 `/scratch/stefan/7921156/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H](C)[NH+](C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051973.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051973 none CC(CNC(=O)[C@H](C)[NH+](C)C)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 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, 1, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [10, 7, 10, 14, 23, 23, 23, 26, 26, 26, 26, 26, 26, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 14, 14, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 1] 26 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: 99 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051973 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005051973/1 /scratch/stefan/7921156/working/building/REAL250005051973 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/91 `/scratch/stefan/7921156/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H](C)N(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051973.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005051973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051973/1/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: REAL250005051973 none CC(CNC(=O)[C@H](C)N(C)C)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 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 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 41, 96, 96, 96, 150, 150, 150, 156, 156, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 41, 41, 96, 150, 150, 150, 156, 156, 156, 156, 156, 156, 8, 1] 156 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 612 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051973 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051973 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051973/0.* 1: /scratch/stefan/7921156/working/building/REAL250005051973/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051973 Building REAL250005051974 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051974' /scratch/stefan/7921156/working/building/REAL250005051974 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051974 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051974/0 /scratch/stefan/7921156/working/building/REAL250005051974 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/92 `/scratch/stefan/7921156/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(F)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051974.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051974 none CCC=C(F)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 114, 154, 114, 114, 61, 20, 8, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 154, 114, 61, 61, 20, 20, 20, 20, 8, 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: 801 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051974 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051974 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051974/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051974 Building REAL250005051975 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051975' /scratch/stefan/7921156/working/building/REAL250005051975 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051975 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051975/0 /scratch/stefan/7921156/working/building/REAL250005051975 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/93 `/scratch/stefan/7921156/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051975.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051975 none CCC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 166, 166, 111, 111, 111, 55, 20, 7, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 166, 166, 111, 55, 55, 20, 20, 20, 20, 7, 1] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 771 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051975 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051975 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051975/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051975 Building REAL250005051976 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051976' /scratch/stefan/7921156/working/building/REAL250005051976 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005051976 as failed and skipping /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `/scratch/stefan/7921156/failed' `/scratch/stefan/7921156/working/building/REAL250005051976' -> `/scratch/stefan/7921156/failed/REAL250005051976' Building REAL250005051977 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051977' /scratch/stefan/7921156/working/building/REAL250005051977 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051977 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051977/0 /scratch/stefan/7921156/working/building/REAL250005051977 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/94 `/scratch/stefan/7921156/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCC(=O)N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051977.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051977 none CC(CNC(=O)C1CCC(=O)N1)NC(=O)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.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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] 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: [144, 66, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 144, 179, 179, 179, 188, 188, 188, 188, 188, 144, 144, 144, 144, 66, 66, 12, 1, 1, 1, 1, 1, 1, 179, 188] 188 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 28, 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, 34, 35]) total number of confs: 743 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: REAL250005051977 none CC(CNC(=O)C1CCC(=O)N1)NC(=O)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.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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] 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: [23, 11, 23, 62, 129, 129, 129, 188, 188, 188, 188, 188, 11, 1, 11, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 62, 62, 129, 188, 188, 188, 188, 188, 188, 11, 1] 188 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: 653 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051977 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051977 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051977/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051977 Building REAL250005051978 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051978' /scratch/stefan/7921156/working/building/REAL250005051978 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051978 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051978/0 /scratch/stefan/7921156/working/building/REAL250005051978 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/95 `/scratch/stefan/7921156/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)(C)CO)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051978.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051978 none CC(CNC(=O)C(C)(C)CO)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 18, 49, 115, 115, 115, 189, 189, 189, 201, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 49, 49, 115, 189, 189, 189, 189, 189, 189, 201, 201, 603, 9, 1] 603 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1403 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051978 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051978 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051978/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051978 Building REAL250005051979 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051979' /scratch/stefan/7921156/working/building/REAL250005051979 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051979 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051979/0 /scratch/stefan/7921156/working/building/REAL250005051979 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/96 `/scratch/stefan/7921156/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=NC=CN1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051979.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051979 none CC(CNC(=O)C1=NC=CN1C)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [59, 37, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 59, 71, 71, 71, 71, 71, 71, 71, 71, 59, 59, 59, 59, 37, 37, 12, 1, 1, 2, 2, 2, 71, 71] 71 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 278 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: REAL250005051979 none CC(CNC(=O)C1=NC=CN1C)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 12, 27, 60, 60, 60, 71, 71, 71, 71, 71, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 27, 60, 71, 71, 71, 71, 71, 5, 1] 71 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: 228 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051979 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051979 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051979/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051979 Building REAL250005051980 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051980' /scratch/stefan/7921156/working/building/REAL250005051980 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051980 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051980/0 /scratch/stefan/7921156/working/building/REAL250005051980 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/97 `/scratch/stefan/7921156/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC(O)C1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051980.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051980 none CC(CNC(=O)CC(O)C1CC1)NC(=O)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, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [189, 154, 61, 61, 17, 61, 5, 1, 5, 1, 1, 1, 189, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 189, 189, 154, 154, 61, 17, 17, 5, 15, 1, 1, 1, 1, 1, 201, 201] 603 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38]) total number of confs: 829 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051980 none CC(CNC(=O)CC(O)C1CC1)NC(=O)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, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 10, 26, 61, 61, 61, 145, 160, 160, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 26, 26, 61, 145, 145, 160, 480, 201, 201, 201, 201, 201, 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: 1273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051980 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051980 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051980/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051980 Building REAL250005051981 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051981' /scratch/stefan/7921156/working/building/REAL250005051981 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051981 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051981/0 /scratch/stefan/7921156/working/building/REAL250005051981 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/98 `/scratch/stefan/7921156/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC1CC1)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051981.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051981 none CC(=CC1CC1)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 5, 28, 28, 28, 101, 174, 174, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1, 28, 101, 101, 174, 174, 174, 174, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 25, 26, 27, 28, 29] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 815 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: REAL250005051981 none CC(=CC1CC1)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 69, 136, 136, 201, 201, 69, 69, 34, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 201, 201, 201, 201, 201, 69, 34, 34, 14, 14, 14, 14, 4, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 704 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051981 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051981 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051981/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051981 Building REAL250005051982 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051982' /scratch/stefan/7921156/working/building/REAL250005051982 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051982 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051982/0 /scratch/stefan/7921156/working/building/REAL250005051982 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/99 `/scratch/stefan/7921156/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCC=CO1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051982.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051982 none CC(CNC(=O)C1CCC=CO1)NC(=O)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.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [138, 69, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 138, 161, 161, 161, 167, 167, 167, 167, 167, 138, 138, 138, 138, 69, 69, 13, 1, 1, 1, 1, 1, 1, 1, 161, 167] 167 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 28, 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, 35, 36]) total number of confs: 671 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: REAL250005051982 none CC(CNC(=O)C1CCC=CO1)NC(=O)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.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 9, 20, 47, 94, 94, 94, 167, 167, 167, 167, 167, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 47, 47, 94, 167, 167, 167, 167, 167, 167, 167, 9, 1] 167 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: 549 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051982 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051982 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051982/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051982 Building REAL250005051983 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051983' /scratch/stefan/7921156/working/building/REAL250005051983 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051983 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051983/0 /scratch/stefan/7921156/working/building/REAL250005051983 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/100 `/scratch/stefan/7921156/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CSC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051983.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051983 none CC(CNC(=O)CC1CSC1)NC(=O)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', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 14, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 121, 40, 40, 7, 40, 1, 1, 1, 1, 1, 179, 200, 200, 200, 201, 201, 201, 201, 201, 179, 179, 179, 179, 121, 121, 40, 7, 7, 1, 1, 1, 1, 1, 200, 201] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 29, 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, 34, 35]) total number of confs: 815 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: REAL250005051983 none CC(CNC(=O)CC1CSC1)NC(=O)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', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 14, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 42, 107, 107, 107, 168, 201, 201, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 42, 42, 107, 168, 168, 201, 201, 201, 201, 201, 6, 1] 201 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 780 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051983 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051983 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051983/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051983 Building REAL250005051984 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051984' /scratch/stefan/7921156/working/building/REAL250005051984 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051984 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051984/0 /scratch/stefan/7921156/working/building/REAL250005051984 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/101 `/scratch/stefan/7921156/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(F)CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051984.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051984 none CC(CNC(=O)C1(F)CCC1)NC(=O)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.2', 'O.2', 'C.2', 'C.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, 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 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [128, 64, 11, 11, 1, 11, 1, 1, 1, 1, 1, 128, 153, 154, 153, 161, 161, 161, 161, 161, 128, 128, 128, 128, 64, 64, 11, 1, 1, 1, 1, 1, 1, 154, 161] 161 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 27, 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, 33, 34]) total number of confs: 647 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: REAL250005051984 none CC(CNC(=O)C1(F)CCC1)NC(=O)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.2', 'O.2', 'C.2', 'C.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, 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 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 22, 48, 110, 110, 110, 161, 161, 161, 161, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 48, 48, 110, 161, 161, 161, 161, 161, 161, 10, 1] 161 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: 544 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051984 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051984 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051984/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051984 Building REAL250005051985 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051985' /scratch/stefan/7921156/working/building/REAL250005051985 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051985 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051985/0 /scratch/stefan/7921156/working/building/REAL250005051985 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/102 `/scratch/stefan/7921156/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CC(N)=O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051985.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051985 none CC(CNC(=O)C=CC(N)=O)NC(=O)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.2', 'O.2', 'C.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, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 48, 105, 105, 105, 180, 180, 201, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 48, 48, 105, 180, 180, 200, 201, 6, 1] 201 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 667 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051985 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051985 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051985/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051985 Building REAL250005051986 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051986' /scratch/stefan/7921156/working/building/REAL250005051986 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051986 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051986/0 /scratch/stefan/7921156/working/building/REAL250005051986 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/103 `/scratch/stefan/7921156/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCSCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051986.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051986 none C#CCSCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 105, 51, 51, 51, 16, 6, 3, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 105, 105, 51, 16, 16, 6, 6, 6, 6, 3, 1] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051986 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051986 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051986/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051986 Building REAL250005051987 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051987' /scratch/stefan/7921156/working/building/REAL250005051987 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051987 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051987/0 /scratch/stefan/7921156/working/building/REAL250005051987 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/104 `/scratch/stefan/7921156/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051987.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051987 none CC(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 399 conformations in input total number of sets (complete confs): 399 using faster count positions algorithm for large data unique positions, atoms: [133, 125, 132, 125, 125, 73, 27, 10, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 399, 125, 73, 73, 27, 27, 27, 27, 10, 1] 399 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: 905 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051987 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051987 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051987/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051987 Building REAL250005051988 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051988' /scratch/stefan/7921156/working/building/REAL250005051988 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051988 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051988/0 /scratch/stefan/7921156/working/building/REAL250005051988 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/105 `/scratch/stefan/7921156/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(O)CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051988.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051988 none CC(CNC(=O)C1(O)CCC1)NC(=O)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, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 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 444 conformations in input total number of sets (complete confs): 444 using faster count positions algorithm for large data unique positions, atoms: [117, 60, 11, 11, 1, 11, 1, 1, 1, 1, 1, 117, 142, 142, 142, 148, 148, 148, 148, 148, 117, 117, 117, 117, 60, 60, 11, 6, 1, 1, 1, 1, 1, 1, 142, 148] 444 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]) total number of confs: 596 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: REAL250005051988 none CC(CNC(=O)C1(O)CCC1)NC(=O)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, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 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 444 conformations in input total number of sets (complete confs): 444 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 19, 50, 102, 102, 102, 148, 148, 148, 148, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 50, 50, 102, 444, 148, 148, 148, 148, 148, 148, 9, 1] 444 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: 949 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051988 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051988 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051988/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051988 Building REAL250005051989 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051989' /scratch/stefan/7921156/working/building/REAL250005051989 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051989 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051989/0 /scratch/stefan/7921156/working/building/REAL250005051989 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/106 `/scratch/stefan/7921156/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(O)C1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051989.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051989 none CC(CNC(=O)C(O)C1CC1)NC(=O)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, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [180, 129, 43, 43, 7, 43, 1, 7, 1, 1, 1, 180, 201, 201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 180, 129, 129, 43, 7, 21, 1, 1, 1, 1, 1, 201, 201] 603 rigid atoms, others: [32, 33, 6, 8, 9, 10, 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, 28, 34, 35]) total number of confs: 827 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: REAL250005051989 none CC(CNC(=O)C(O)C1CC1)NC(=O)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, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 12, 31, 85, 85, 85, 174, 174, 201, 201, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 31, 31, 85, 174, 522, 201, 201, 201, 201, 201, 5, 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: 1307 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051989 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051989 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051989/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051989 Building REAL250005051990 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051990' /scratch/stefan/7921156/working/building/REAL250005051990 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051990 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051990/0 /scratch/stefan/7921156/working/building/REAL250005051990 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/107 `/scratch/stefan/7921156/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN1C=NN=C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051990.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051990 none CC(CNC(=O)CN1C=NN=C1)NC(=O)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.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 1, 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, 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: [175, 123, 40, 40, 8, 40, 1, 1, 1, 1, 1, 1, 175, 195, 195, 195, 201, 201, 201, 201, 201, 175, 175, 175, 175, 123, 123, 40, 8, 8, 1, 1, 195, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 30, 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, 32, 33]) total number of confs: 821 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051990 none CC(CNC(=O)CN1C=NN=C1)NC(=O)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.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 1, 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, 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: [16, 8, 16, 43, 99, 99, 99, 197, 201, 201, 201, 201, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 43, 43, 99, 197, 197, 201, 201, 8, 1] 201 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 766 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051990 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051990 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051990/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051990 Building REAL250005051991 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051991' /scratch/stefan/7921156/working/building/REAL250005051991 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051991 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051991/0 /scratch/stefan/7921156/working/building/REAL250005051991 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/108 `/scratch/stefan/7921156/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051991.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051991 none C=CCC(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 150, 83, 150, 83, 83, 41, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 150, 150, 150, 150, 83, 41, 41, 14, 14, 14, 14, 4, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 871 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051991 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051991 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051991/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051991 Building REAL250005051992 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051992' /scratch/stefan/7921156/working/building/REAL250005051992 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051992 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051992/0 /scratch/stefan/7921156/working/building/REAL250005051992 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/109 `/scratch/stefan/7921156/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC1F)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051992.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051992 none CC(CNC(=O)C1CC1F)NC(=O)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.2', 'O.2', 'C.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, 5, 5, 15, 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: [154, 69, 13, 13, 1, 13, 1, 1, 1, 1, 156, 191, 191, 191, 201, 201, 201, 201, 201, 156, 156, 156, 156, 69, 69, 13, 1, 1, 1, 1, 191, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 793 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: REAL250005051992 none CC(CNC(=O)C1CC1F)NC(=O)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.2', 'O.2', 'C.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, 5, 5, 15, 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: [22, 9, 22, 66, 138, 138, 138, 201, 201, 201, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 66, 66, 138, 201, 201, 201, 201, 9, 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: 674 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051992 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051992 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051992/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051992 Building REAL250005051993 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051993' /scratch/stefan/7921156/working/building/REAL250005051993 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005051993 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051993/0 /scratch/stefan/7921156/working/building/REAL250005051993 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/110 `/scratch/stefan/7921156/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H](C)[NH+](C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051993.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051993 none CC(CNC(=O)[C@H](C)[NH+](C)C)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 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, 1, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [10, 7, 10, 14, 23, 23, 23, 26, 26, 26, 26, 26, 26, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 14, 14, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 1] 26 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: 99 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051993 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005051993/1 /scratch/stefan/7921156/working/building/REAL250005051993 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/111 `/scratch/stefan/7921156/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H](C)N(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051993.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005051993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051993/1/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: REAL250005051993 none CC(CNC(=O)[C@H](C)N(C)C)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 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 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 41, 96, 96, 96, 150, 150, 150, 156, 156, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 41, 41, 96, 150, 150, 150, 156, 156, 156, 156, 156, 156, 8, 1] 156 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 612 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051993 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051993 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051993/0.* 1: /scratch/stefan/7921156/working/building/REAL250005051993/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051993 Building REAL250005051994 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051994' /scratch/stefan/7921156/working/building/REAL250005051994 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051994 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051994/0 /scratch/stefan/7921156/working/building/REAL250005051994 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/112 `/scratch/stefan/7921156/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCF)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051994.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051994 none CC(CNC(=O)CCF)NC(=O)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.2', 'O.2', 'C.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, 5, 15, 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, 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: [19, 7, 19, 53, 114, 114, 114, 196, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 53, 53, 114, 196, 196, 201, 201, 7, 1] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 816 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051994 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051994 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051994/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051994 Building REAL250005051995 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051995' /scratch/stefan/7921156/working/building/REAL250005051995 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051995 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051995/0 /scratch/stefan/7921156/working/building/REAL250005051995 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/113 `/scratch/stefan/7921156/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN1C=CN=N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051995.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051995 none CC(CNC(=O)CN1C=CN=N1)NC(=O)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.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 8, 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, 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: [171, 131, 49, 49, 8, 49, 1, 1, 1, 1, 1, 1, 171, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 171, 171, 131, 131, 49, 8, 8, 1, 1, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 30, 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, 32, 33]) total number of confs: 814 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051995 none CC(CNC(=O)CN1C=CN=N1)NC(=O)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.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 8, 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, 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: [10, 5, 10, 26, 69, 69, 69, 179, 201, 201, 201, 201, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 26, 26, 69, 179, 179, 201, 201, 5, 1] 201 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 708 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051995 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051995 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051995/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051995 Building REAL250005051996 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051996' /scratch/stefan/7921156/working/building/REAL250005051996 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051996 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051996/0 /scratch/stefan/7921156/working/building/REAL250005051996 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/114 `/scratch/stefan/7921156/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005051996.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051996 none C=CC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 7, 7, 7, 39, 120, 120, 185, 185, 185, 201, 201, 201, 201, 201, 1, 1, 1, 6, 6, 6, 7, 39, 39, 120, 120, 120, 120, 185, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 36, 37, 35, 33, 34, 18, 19, 20, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 759 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: REAL250005051996 none C=CC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 109, 109, 109, 56, 15, 4, 15, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 109, 56, 56, 15, 15, 15, 15, 4, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 650 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051996 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051996 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051996/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051996 Building REAL250005051997 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051997' /scratch/stefan/7921156/working/building/REAL250005051997 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051997 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051997/0 /scratch/stefan/7921156/working/building/REAL250005051997 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/115 `/scratch/stefan/7921156/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(O)COC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051997.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051997 none CC(CNC(=O)C1(O)COC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 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] 1 hydrogens need rotated 423 conformations in input total number of sets (complete confs): 423 using faster count positions algorithm for large data unique positions, atoms: [114, 56, 12, 12, 1, 12, 1, 1, 1, 1, 1, 114, 135, 135, 135, 141, 141, 141, 141, 141, 114, 114, 114, 114, 56, 56, 12, 6, 1, 1, 1, 1, 135, 141] 423 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]) total number of confs: 559 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: REAL250005051997 none CC(CNC(=O)C1(O)COC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 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] 1 hydrogens need rotated 423 conformations in input total number of sets (complete confs): 423 using faster count positions algorithm for large data unique positions, atoms: [20, 9, 20, 50, 97, 97, 97, 141, 141, 141, 141, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 50, 50, 97, 423, 141, 141, 141, 141, 9, 1] 423 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: 907 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051997 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051997 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051997/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051997 Building REAL250005051998 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051998' /scratch/stefan/7921156/working/building/REAL250005051998 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051998 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051998/0 /scratch/stefan/7921156/working/building/REAL250005051998 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/116 `/scratch/stefan/7921156/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005051998.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051998 none CCC(C)C(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 195, 142, 195, 108, 142, 108, 108, 48, 18, 6, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 195, 195, 195, 195, 142, 426, 108, 48, 48, 18, 18, 18, 18, 6, 1] 603 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1284 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051998 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051998 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051998/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051998 Building REAL250005051999 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005051999' /scratch/stefan/7921156/working/building/REAL250005051999 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005051999 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005051999/0 /scratch/stefan/7921156/working/building/REAL250005051999 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/117 `/scratch/stefan/7921156/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1)=C1CC1) `REAL250005051999.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005051999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005051999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005051999 none CC(C(=O)NCC(C)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 118, 118, 118, 61, 24, 9, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 169, 169, 118, 61, 61, 24, 24, 24, 24, 9, 1, 169, 169, 169, 169] 169 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: 576 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: REAL250005051999 none CC(C(=O)NCC(C)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [1, 1, 1, 12, 12, 13, 60, 125, 127, 159, 159, 159, 169, 169, 169, 169, 169, 1, 1, 1, 2, 2, 2, 13, 60, 60, 127, 127, 127, 127, 159, 169, 1, 1, 1, 1] 169 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 17, 18, 19] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 664 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005051999 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005051999 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005051999/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005051999 Building REAL250005052000 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052000' /scratch/stefan/7921156/working/building/REAL250005052000 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052000 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052000/0 /scratch/stefan/7921156/working/building/REAL250005052000 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/118 `/scratch/stefan/7921156/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052000.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052000 none CCC1CC1C(=O)NCC(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 1, 1, 1, 1, 10, 10, 10, 46, 108, 111, 152, 152, 152, 164, 164, 164, 164, 164, 2, 2, 2, 2, 2, 1, 1, 1, 1, 10, 46, 46, 111, 111, 111, 111, 152, 164] 164 rigid atoms, others: [1, 2, 3, 4, 5, 25, 26, 27, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 635 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: REAL250005052000 none CCC1CC1C(=O)NCC(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 118, 118, 118, 59, 23, 10, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 164, 164, 164, 164, 118, 59, 59, 23, 23, 23, 23, 10, 1] 164 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: 563 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052000 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052000 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052000/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052000 Building REAL250005052001 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052001' /scratch/stefan/7921156/working/building/REAL250005052001 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052001 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052001/0 /scratch/stefan/7921156/working/building/REAL250005052001 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/119 `/scratch/stefan/7921156/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052001.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052001 none CC(O)CCCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [188, 157, 201, 120, 107, 34, 34, 34, 19, 8, 4, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 147, 156, 141, 141, 107, 107, 34, 19, 19, 8, 8, 8, 8, 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: 1712 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052001 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052001 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052001/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052001 Building REAL250005052002 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052002' /scratch/stefan/7921156/working/building/REAL250005052002 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052002 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052002/0 /scratch/stefan/7921156/working/building/REAL250005052002 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/120 `/scratch/stefan/7921156/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1(O)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052002.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052002 none CC(CNC(=O)CC1(O)CC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 4, 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: [186, 126, 36, 36, 9, 36, 1, 1, 1, 1, 1, 186, 201, 201, 201, 201, 201, 201, 201, 201, 186, 186, 186, 186, 126, 126, 36, 9, 9, 6, 1, 1, 1, 1, 201, 201] 603 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]) total number of confs: 829 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: REAL250005052002 none CC(CNC(=O)CC1(O)CC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 4, 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: [12, 4, 12, 38, 91, 91, 91, 182, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 38, 38, 91, 182, 182, 603, 201, 201, 201, 201, 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: 1366 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052002 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052002 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052002/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052002 Building REAL250005052003 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052003' /scratch/stefan/7921156/working/building/REAL250005052003 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052003 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052003/0 /scratch/stefan/7921156/working/building/REAL250005052003 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/121 `/scratch/stefan/7921156/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CCF)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052003.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052003 none CC(CNC(=O)C=CCF)NC(=O)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.2', 'O.2', 'C.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, 5, 15, 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: [16, 6, 16, 53, 116, 116, 116, 179, 179, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 53, 53, 116, 179, 179, 201, 201, 6, 1] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 749 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052003 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052003 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052003/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052003 Building REAL250005052004 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052004' /scratch/stefan/7921156/working/building/REAL250005052004 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052004 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052004/0 /scratch/stefan/7921156/working/building/REAL250005052004 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/122 `/scratch/stefan/7921156/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(F)CC1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052004.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052004 none CC(CNC(=O)C(F)CC1CC1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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: [192, 162, 62, 62, 14, 62, 3, 14, 1, 1, 1, 1, 192, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 192, 192, 162, 162, 62, 14, 3, 3, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37]) total number of confs: 806 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052004 none CC(CNC(=O)C(F)CC1CC1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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: [8, 4, 8, 20, 52, 52, 52, 132, 132, 166, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 20, 20, 52, 132, 166, 166, 201, 201, 201, 201, 201, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 827 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052004 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052004 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052004/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052004 Building REAL250005052005 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052005' /scratch/stefan/7921156/working/building/REAL250005052005 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052005 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052005/0 /scratch/stefan/7921156/working/building/REAL250005052005 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/123 `/scratch/stefan/7921156/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1)OC) `REAL250005052005.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052005 none CCC(CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 120, 64, 64, 64, 26, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 187, 194, 201, 201, 201, 201, 201, 187, 120, 120, 64, 26, 26, 11, 11, 11, 11, 4, 1, 194, 194, 194] 201 rigid atoms, others: [37, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 912 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052005 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052005 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052005/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052005 Building REAL250005052006 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052006' /scratch/stefan/7921156/working/building/REAL250005052006 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052006 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052006/0 /scratch/stefan/7921156/working/building/REAL250005052006 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/124 `/scratch/stefan/7921156/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=C(Cl)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052006.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052006 none CC(CNC(=O)C1=C(Cl)CC1)NC(=O)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', 'Cl', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 16, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [149, 65, 13, 13, 1, 13, 1, 1, 1, 1, 1, 150, 192, 192, 192, 194, 194, 194, 194, 194, 150, 150, 150, 150, 65, 65, 13, 1, 1, 1, 1, 192, 194] 194 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27, 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, 31, 32]) total number of confs: 768 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052006 none CC(CNC(=O)C1=C(Cl)CC1)NC(=O)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', 'Cl', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 16, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 19, 65, 128, 128, 128, 194, 194, 194, 194, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 65, 65, 128, 194, 194, 194, 194, 7, 1] 194 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: 544 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052006 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052006 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052006/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052006 Building REAL250005052007 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052007' /scratch/stefan/7921156/working/building/REAL250005052007 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052007 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052007/0 /scratch/stefan/7921156/working/building/REAL250005052007 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/125 `/scratch/stefan/7921156/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@]12C[C@H]1[C@H](F)C2)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052007.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052007 none CC(CNC(=O)[C@]12C[C@H]1[C@H](F)C2)NC(=O)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', 'H', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 15, 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, 7, 7, 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: [132, 42, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 133, 193, 195, 193, 201, 201, 201, 201, 201, 133, 133, 133, 133, 42, 42, 7, 1, 1, 1, 1, 195, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 778 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: REAL250005052007 none CC(CNC(=O)[C@]12C[C@H]1[C@H](F)C2)NC(=O)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', 'H', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 15, 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, 7, 7, 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: [21, 8, 21, 62, 117, 117, 117, 201, 201, 201, 201, 201, 201, 201, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 62, 62, 117, 201, 201, 201, 201, 8, 1] 201 rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 531 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052007 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052007 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052007/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052007 Building REAL250005052008 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052008' /scratch/stefan/7921156/working/building/REAL250005052008 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052008 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052008/0 /scratch/stefan/7921156/working/building/REAL250005052008 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/126 `/scratch/stefan/7921156/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCCOC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052008.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052008 none CC(CNC(=O)C1=CCCOC1)NC(=O)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: [152, 60, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 153, 191, 192, 191, 201, 201, 201, 201, 201, 153, 153, 153, 153, 60, 60, 12, 1, 1, 1, 1, 1, 1, 1, 192, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 28, 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, 35, 36]) total number of confs: 801 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: REAL250005052008 none CC(CNC(=O)C1=CCCOC1)NC(=O)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: [18, 7, 18, 58, 116, 116, 116, 201, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 58, 58, 116, 201, 201, 201, 201, 201, 201, 201, 7, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 535 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052008 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052008 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052008/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052008 Building REAL250005052009 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052009' /scratch/stefan/7921156/working/building/REAL250005052009 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052009 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052009/0 /scratch/stefan/7921156/working/building/REAL250005052009 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/127 `/scratch/stefan/7921156/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(O)C(C)(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052009.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052009 none CC(CNC(=O)C(O)C(C)(C)C)NC(=O)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', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 246 conformations in input total number of sets (complete confs): 246 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 19, 37, 70, 70, 70, 82, 82, 82, 82, 82, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 37, 37, 70, 82, 246, 82, 82, 82, 82, 82, 82, 82, 82, 82, 9, 1] 246 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 557 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052009 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052009 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052009/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052009 Building REAL250005052010 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052010' /scratch/stefan/7921156/working/building/REAL250005052010 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052010 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052010/0 /scratch/stefan/7921156/working/building/REAL250005052010 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/128 `/scratch/stefan/7921156/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052010.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052010 none C#CCCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 109, 109, 109, 53, 18, 7, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 188, 188, 109, 53, 53, 18, 18, 18, 18, 7, 1] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 821 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052010 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052010 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052010/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052010 Building REAL250005052011 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052011' /scratch/stefan/7921156/working/building/REAL250005052011 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052011 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052011/0 /scratch/stefan/7921156/working/building/REAL250005052011 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/129 `/scratch/stefan/7921156/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN1CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052011.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052011 none CC(CNC(=O)CN1CCC1)NC(=O)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'] 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, 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: [187, 127, 38, 38, 6, 38, 1, 1, 1, 1, 1, 187, 200, 200, 200, 201, 201, 201, 201, 201, 187, 187, 187, 187, 127, 127, 38, 6, 6, 1, 1, 1, 1, 1, 1, 200, 201] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 29, 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, 35, 36]) total number of confs: 800 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: REAL250005052011 none CC(CNC(=O)CN1CCC1)NC(=O)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'] 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, 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: [15, 6, 15, 43, 109, 109, 109, 188, 201, 201, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 43, 43, 109, 188, 188, 201, 201, 201, 201, 201, 201, 6, 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: 761 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052011 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052011/1 /scratch/stefan/7921156/working/building/REAL250005052011 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/130 `/scratch/stefan/7921156/working/3D/130' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C[NH+]1CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052011.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052011/1/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: REAL250005052011 none CC(CNC(=O)C[NH+]1CCC1)NC(=O)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'] 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, 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] 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: [22, 18, 14, 14, 6, 14, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 24, 24, 24, 24, 24, 22, 22, 22, 22, 18, 18, 14, 6, 6, 1, 1, 1, 1, 1, 1, 22, 24] 24 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 30, 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, 36, 37]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052011 none CC(CNC(=O)C[NH+]1CCC1)NC(=O)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'] 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, 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] 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: [9, 7, 9, 12, 18, 18, 18, 23, 24, 24, 24, 24, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 12, 12, 18, 23, 23, 24, 24, 24, 24, 24, 24, 7, 1] 24 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: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052011 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052011 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052011/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052011/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052011 Building REAL250005052012 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052012' /scratch/stefan/7921156/working/building/REAL250005052012 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052012 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052012/0 /scratch/stefan/7921156/working/building/REAL250005052012 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/131 `/scratch/stefan/7921156/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(O)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052012.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052012 none CC(C)C(O)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 172, 201, 140, 172, 82, 82, 82, 33, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 172, 516, 140, 140, 82, 33, 33, 12, 12, 12, 12, 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: 1414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052012 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052012 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052012/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052012 Building REAL250005052013 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052013' /scratch/stefan/7921156/working/building/REAL250005052013 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052013 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052013/0 /scratch/stefan/7921156/working/building/REAL250005052013 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/132 `/scratch/stefan/7921156/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052013.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052013 none CCCC(C)(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 155, 120, 155, 155, 120, 120, 51, 18, 5, 18, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 155, 155, 155, 465, 120, 51, 51, 18, 18, 18, 18, 5, 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: 1309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052013 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052013 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052013/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052013 Building REAL250005052014 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052014' /scratch/stefan/7921156/working/building/REAL250005052014 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052014 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052014/0 /scratch/stefan/7921156/working/building/REAL250005052014 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/133 `/scratch/stefan/7921156/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052014.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052014 none CCOC(C)(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 126, 186, 186, 126, 126, 47, 18, 5, 18, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 186, 186, 186, 186, 186, 186, 126, 47, 47, 18, 18, 18, 18, 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: 754 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052014 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052014 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052014/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052014 Building REAL250005052015 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052015' /scratch/stefan/7921156/working/building/REAL250005052015 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052015 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052015/0 /scratch/stefan/7921156/working/building/REAL250005052015 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/134 `/scratch/stefan/7921156/working/3D/134' -> `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)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052015.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052015 none C#C[C@H]1C[C@H]1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 42, 103, 104, 139, 139, 139, 153, 153, 153, 153, 153, 1, 1, 1, 9, 42, 42, 104, 104, 104, 104, 139, 153] 153 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 585 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: REAL250005052015 none C#C[C@H]1C[C@H]1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 153, 153, 120, 153, 120, 120, 65, 26, 10, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 153, 153, 153, 120, 65, 65, 26, 26, 26, 26, 11, 1] 153 rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 544 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052015 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052015 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052015/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052015 Building REAL250005052016 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052016' /scratch/stefan/7921156/working/building/REAL250005052016 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052016 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052016/0 /scratch/stefan/7921156/working/building/REAL250005052016 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/135 `/scratch/stefan/7921156/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(N=[N+]=[N-])CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052016.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052016 none CC(CNC(=O)C1(N=[N+]=[N-])CC1)NC(=O)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.2', 'N.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 60, 12, 12, 1, 12, 1, 1, 11, 11, 1, 1, 117, 159, 159, 159, 164, 164, 164, 164, 164, 117, 117, 117, 117, 60, 60, 12, 1, 1, 1, 1, 159, 164] 201 rigid atoms, others: [4, 6, 7, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33]) total number of confs: 661 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: REAL250005052016 none CC(CNC(=O)C1(N=[N+]=[N-])CC1)NC(=O)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.2', 'N.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 27, 75, 75, 75, 164, 201, 201, 164, 164, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 27, 75, 164, 164, 164, 164, 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: 553 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052016 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052016 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052016/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052016 Building REAL250005052017 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052017' /scratch/stefan/7921156/working/building/REAL250005052017 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052017 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052017/0 /scratch/stefan/7921156/working/building/REAL250005052017 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/136 `/scratch/stefan/7921156/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CNC(=O)O1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052017.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052017 none CC(CNC(=O)C1=CNC(=O)O1)NC(=O)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.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [97, 52, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 97, 121, 121, 121, 130, 130, 130, 130, 130, 97, 97, 97, 97, 52, 52, 12, 1, 1, 121, 130] 130 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 488 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: REAL250005052017 none CC(CNC(=O)C1=CNC(=O)O1)NC(=O)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.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [21, 10, 21, 55, 105, 105, 105, 130, 130, 130, 130, 130, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 55, 55, 105, 130, 130, 10, 1] 130 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 416 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052017 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052017 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052017/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052017 Building REAL250005052018 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052018' /scratch/stefan/7921156/working/building/REAL250005052018 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052018 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052018/0 /scratch/stefan/7921156/working/building/REAL250005052018 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/137 `/scratch/stefan/7921156/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1C[C@H]1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052018.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052018 none CC(C)[C@@H]1C[C@H]1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 65, 159, 160, 195, 195, 195, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 4, 4, 1, 1, 12, 65, 65, 160, 160, 160, 160, 195, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 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: REAL250005052018 none CC(C)[C@@H]1C[C@H]1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 106, 201, 106, 106, 49, 16, 7, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 49, 49, 16, 16, 16, 16, 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: 646 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052018 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052018 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052018/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052018 Building REAL250005052019 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052019' /scratch/stefan/7921156/working/building/REAL250005052019 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052019 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052019/0 /scratch/stefan/7921156/working/building/REAL250005052019 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/138 `/scratch/stefan/7921156/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1C2CCC21)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052019.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052019 none CC(CNC(=O)C1C2CCC21)NC(=O)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'] 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, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [104, 48, 10, 10, 1, 10, 1, 1, 1, 1, 1, 106, 145, 145, 145, 151, 151, 151, 151, 151, 106, 106, 106, 106, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 145, 151] 151 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 27, 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, 34, 35]) total number of confs: 579 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: REAL250005052019 none CC(CNC(=O)C1C2CCC21)NC(=O)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'] 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, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [22, 8, 22, 66, 123, 123, 123, 151, 151, 151, 151, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 66, 66, 123, 151, 151, 151, 151, 151, 151, 151, 8, 1] 151 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: 532 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052019 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052019 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052019/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052019 Building REAL250005052020 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052020' /scratch/stefan/7921156/working/building/REAL250005052020 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052020 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052020/0 /scratch/stefan/7921156/working/building/REAL250005052020 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/139 `/scratch/stefan/7921156/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052020.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052020 none C=C1CCC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 11, 47, 89, 92, 120, 120, 120, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 1, 11, 47, 47, 92, 92, 92, 92, 120, 130] 130 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 512 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: REAL250005052020 none C=C1CCC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 105, 105, 105, 55, 20, 9, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 105, 55, 55, 20, 20, 20, 20, 9, 1] 130 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: 459 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052020 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052020 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052020/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052020 Building REAL250005052021 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052021' /scratch/stefan/7921156/working/building/REAL250005052021 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052021 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052021/0 /scratch/stefan/7921156/working/building/REAL250005052021 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/140 `/scratch/stefan/7921156/working/3D/140' -> `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)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052021.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052021 none CC(CNC(=O)C1[C@H](C)[C@@H]1C)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 7, 5, 5, 7, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [119, 44, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 121, 171, 171, 171, 178, 178, 178, 178, 178, 121, 121, 121, 121, 44, 44, 8, 1, 2, 2, 2, 2, 2, 2, 171, 178] 178 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 5, 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: 696 number of broken/clashed sets: 178 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052021 none CC(CNC(=O)C1[C@H](C)[C@@H]1C)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 7, 5, 5, 7, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [27, 8, 27, 75, 146, 146, 146, 178, 178, 178, 178, 178, 178, 8, 1, 8, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 75, 75, 146, 178, 178, 178, 178, 178, 178, 178, 8, 1] 178 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: 610 number of broken/clashed sets: 178 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052021 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052021 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052021/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052021 Building REAL250005052022 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052022' /scratch/stefan/7921156/working/building/REAL250005052022 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052022 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052022/0 /scratch/stefan/7921156/working/building/REAL250005052022 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/141 `/scratch/stefan/7921156/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H](C)[NH+](C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052022.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052022 none CC(CNC(=O)[C@@H](C)[NH+](C)C)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 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, 1, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 10, 11, 11, 11, 12, 12, 12, 12, 12, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 1] 12 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: 49 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052022 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052022/1 /scratch/stefan/7921156/working/building/REAL250005052022 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/142 `/scratch/stefan/7921156/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H](C)N(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052022.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052022/1/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: REAL250005052022 none CC(CNC(=O)[C@@H](C)N(C)C)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 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 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 22, 47, 106, 106, 106, 163, 163, 163, 171, 171, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 47, 47, 106, 163, 163, 163, 171, 171, 171, 171, 171, 171, 10, 1] 171 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: 642 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052022 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052022 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052022/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052022/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052022 Building REAL250005052023 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052023' /scratch/stefan/7921156/working/building/REAL250005052023 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052023 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052023/0 /scratch/stefan/7921156/working/building/REAL250005052023 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/143 `/scratch/stefan/7921156/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052023.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052023 none CC=CC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 147, 147, 107, 107, 107, 50, 19, 11, 19, 11, 1, 11, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 154, 147, 147, 107, 50, 50, 19, 19, 19, 19, 11, 1] 154 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 519 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052023 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052023 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052023/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052023 Building REAL250005052024 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052024' /scratch/stefan/7921156/working/building/REAL250005052024 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052024 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052024/0 /scratch/stefan/7921156/working/building/REAL250005052024 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/144 `/scratch/stefan/7921156/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=NC=NN1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052024.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052024 none CC(CNC(=O)C1=NC=NN1C)NC(=O)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', '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, 8, 1, 8, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [57, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 57, 68, 68, 68, 71, 71, 71, 71, 71, 57, 57, 57, 57, 35, 35, 11, 1, 2, 2, 2, 68, 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: 263 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: REAL250005052024 none CC(CNC(=O)C1=NC=NN1C)NC(=O)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', '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, 8, 1, 8, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 32, 66, 66, 66, 71, 71, 71, 71, 71, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 32, 32, 66, 71, 71, 71, 71, 7, 1] 71 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: 234 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052024 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052024 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052024/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052024 Building REAL250005052025 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052025' /scratch/stefan/7921156/working/building/REAL250005052025 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052025 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052025/0 /scratch/stefan/7921156/working/building/REAL250005052025 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/145 `/scratch/stefan/7921156/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1CC[C@@H](O)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052025.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052025 none CC(CNC(=O)[C@@H]1CC[C@@H](O)C1)NC(=O)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', 'H', '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, 5, 7, 5, 5, 5, 7, 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, 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: [138, 52, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 139, 193, 193, 193, 201, 201, 201, 201, 201, 139, 139, 139, 139, 52, 52, 10, 1, 1, 1, 1, 6, 1, 1, 193, 201] 603 rigid atoms, others: [32, 33, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 36, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 37, 38]) total number of confs: 785 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052025 none CC(CNC(=O)[C@@H]1CC[C@@H](O)C1)NC(=O)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', 'H', '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, 5, 7, 5, 5, 5, 7, 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, 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: [18, 8, 18, 60, 132, 132, 132, 201, 201, 201, 201, 201, 201, 201, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 60, 60, 132, 201, 201, 201, 201, 603, 201, 201, 8, 1] 603 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: 1283 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052025 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052025 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052025/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052025 Building REAL250005052026 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052026' /scratch/stefan/7921156/working/building/REAL250005052026 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052026 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052026/0 /scratch/stefan/7921156/working/building/REAL250005052026 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/146 `/scratch/stefan/7921156/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1CC=CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052026.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052026 none CC(CNC(=O)[C@@H]1CC=CCC1)NC(=O)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', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 1, 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, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [144, 63, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 147, 191, 191, 191, 201, 201, 201, 201, 201, 147, 147, 147, 147, 63, 63, 12, 1, 1, 1, 1, 1, 1, 1, 1, 191, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38]) total number of confs: 780 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: REAL250005052026 none CC(CNC(=O)[C@@H]1CC=CCC1)NC(=O)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', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 1, 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, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 61, 139, 139, 139, 201, 201, 201, 201, 201, 201, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 61, 61, 139, 201, 201, 201, 201, 201, 201, 201, 201, 9, 1] 201 rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 672 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052026 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052026 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052026/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052026 Building REAL250005052027 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052027' /scratch/stefan/7921156/working/building/REAL250005052027 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052027 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052027/0 /scratch/stefan/7921156/working/building/REAL250005052027 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/147 `/scratch/stefan/7921156/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052027.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052027 none COCC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 123, 123, 53, 53, 53, 23, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 189, 189, 123, 123, 53, 23, 23, 9, 9, 9, 9, 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: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052027 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052027 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052027/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052027 Building REAL250005052028 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052028' /scratch/stefan/7921156/working/building/REAL250005052028 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052028 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052028/0 /scratch/stefan/7921156/working/building/REAL250005052028 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/148 `/scratch/stefan/7921156/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN1CC(C)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052028.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052028 none CC(CNC(=O)CN1CC(C)C1)NC(=O)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: [164, 91, 26, 26, 6, 26, 1, 1, 1, 1, 1, 1, 166, 200, 200, 200, 201, 201, 201, 201, 201, 166, 166, 166, 166, 91, 91, 26, 6, 6, 1, 1, 1, 2, 2, 2, 1, 1, 200, 201] 201 rigid atoms, others: [32, 36, 37, 6, 7, 8, 9, 10, 11, 30, 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, 33, 34, 35, 38, 39]) 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: REAL250005052028 none CC(CNC(=O)CN1CC(C)C1)NC(=O)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: [16, 5, 16, 51, 119, 119, 119, 187, 201, 201, 201, 201, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 51, 51, 119, 187, 187, 201, 201, 201, 201, 201, 201, 201, 201, 5, 1] 201 rigid atoms, others: [39, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 769 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052028 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052028/1 /scratch/stefan/7921156/working/building/REAL250005052028 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/149 `/scratch/stefan/7921156/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C[NH+]1CC(C)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052028.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052028/1/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: REAL250005052028 none CC(CNC(=O)C[NH+]1CC(C)C1)NC(=O)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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 7, 7, 4, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 15, 15, 15, 15, 15, 11, 11, 11, 11, 10, 10, 7, 4, 4, 1, 1, 1, 2, 2, 2, 1, 1, 11, 15] 15 rigid atoms, others: [32, 33, 37, 6, 7, 8, 9, 10, 11, 12, 38, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 39, 40]) 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: REAL250005052028 none CC(CNC(=O)C[NH+]1CC(C)C1)NC(=O)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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 9, 12, 12, 12, 14, 15, 15, 15, 15, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 9, 9, 12, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1] 15 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: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052028 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052028 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052028/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052028/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052028 Building REAL250005052029 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052029' /scratch/stefan/7921156/working/building/REAL250005052029 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052029 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052029/0 /scratch/stefan/7921156/working/building/REAL250005052029 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/150 `/scratch/stefan/7921156/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(C)COC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052029.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052029 none CC(CNC(=O)C1(C)COC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 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, 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 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [124, 42, 6, 6, 1, 6, 1, 1, 1, 1, 1, 126, 167, 168, 167, 178, 178, 178, 178, 178, 126, 126, 126, 126, 42, 42, 6, 2, 2, 2, 1, 1, 1, 1, 168, 178] 178 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 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, 29, 34, 35]) total number of confs: 698 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: REAL250005052029 none CC(CNC(=O)C1(C)COC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 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, 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 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [21, 9, 21, 54, 89, 89, 89, 178, 178, 178, 178, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 54, 54, 89, 178, 178, 178, 178, 178, 178, 178, 9, 1] 178 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: 585 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052029 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052029 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052029/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052029 Building REAL250005052030 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052030' /scratch/stefan/7921156/working/building/REAL250005052030 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052030 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052030/0 /scratch/stefan/7921156/working/building/REAL250005052030 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/151 `/scratch/stefan/7921156/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCCCO1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052030.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052030 none CC(CNC(=O)C1=CCCCO1)NC(=O)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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [127, 61, 12, 11, 1, 11, 1, 1, 1, 1, 1, 1, 128, 156, 156, 156, 159, 159, 159, 159, 159, 128, 128, 128, 128, 61, 61, 12, 1, 1, 1, 1, 1, 1, 1, 156, 159] 159 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 28, 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, 35, 36]) total number of confs: 644 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: REAL250005052030 none CC(CNC(=O)C1=CCCCO1)NC(=O)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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 8, 19, 50, 105, 105, 105, 159, 159, 159, 159, 159, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 50, 50, 105, 159, 159, 159, 159, 159, 159, 159, 8, 1] 159 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 443 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052030 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052030 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052030/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052030 Building REAL250005052031 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052031' /scratch/stefan/7921156/working/building/REAL250005052031 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052031 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052031/0 /scratch/stefan/7921156/working/building/REAL250005052031 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/152 `/scratch/stefan/7921156/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCCS1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052031.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052031 none CC(CNC(=O)C1=CCCS1)NC(=O)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', 'S.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 14, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [115, 58, 12, 12, 1, 12, 1, 1, 1, 1, 1, 115, 140, 140, 140, 144, 144, 144, 144, 144, 115, 115, 115, 115, 58, 58, 12, 1, 1, 1, 1, 1, 140, 144] 144 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27, 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, 32, 33]) total number of confs: 570 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: REAL250005052031 none CC(CNC(=O)C1=CCCS1)NC(=O)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', 'S.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 14, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 53, 104, 104, 104, 144, 144, 144, 144, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 53, 53, 104, 144, 144, 144, 144, 144, 8, 1] 144 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: 435 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052031 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052031 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052031/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052031 Building REAL250005052032 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052032' /scratch/stefan/7921156/working/building/REAL250005052032 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052032 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052032/0 /scratch/stefan/7921156/working/building/REAL250005052032 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/153 `/scratch/stefan/7921156/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052032.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052032 none CC1=NOC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 114, 115, 139, 139, 139, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 11, 50, 50, 115, 115, 115, 115, 139, 145, 1, 1] 145 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 35, 20, 21, 22, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 560 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: REAL250005052032 none CC1=NOC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 145, 121, 121, 121, 57, 24, 10, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 145, 121, 57, 57, 24, 24, 24, 24, 10, 1, 145, 145] 145 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 505 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052032 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052032 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052032/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052032 Building REAL250005052033 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052033' /scratch/stefan/7921156/working/building/REAL250005052033 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052033 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052033/0 /scratch/stefan/7921156/working/building/REAL250005052033 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/154 `/scratch/stefan/7921156/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(=O)NC1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052033.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052033 none CC(CNC(=O)C(=O)NC1CC1)NC(=O)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'] 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, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [163, 121, 37, 37, 6, 37, 6, 6, 1, 1, 1, 1, 163, 183, 183, 183, 187, 187, 187, 187, 187, 163, 163, 163, 163, 121, 121, 37, 6, 1, 1, 1, 1, 1, 183, 187] 187 rigid atoms, others: [32, 33, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 732 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052033 none CC(CNC(=O)C(=O)NC1CC1)NC(=O)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'] 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, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 9, 18, 37, 97, 97, 97, 154, 154, 154, 187, 187, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 37, 37, 97, 154, 187, 187, 187, 187, 187, 9, 1] 187 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: 622 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052033 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052033 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052033/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052033 Building REAL250005052034 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052034' /scratch/stefan/7921156/working/building/REAL250005052034 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052034 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052034/0 /scratch/stefan/7921156/working/building/REAL250005052034 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/155 `/scratch/stefan/7921156/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCSC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052034.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052034 none CC(CNC(=O)C1CCSC1)NC(=O)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', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 14, 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 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [120, 48, 10, 10, 1, 10, 1, 1, 1, 1, 1, 121, 156, 156, 156, 164, 164, 164, 164, 164, 121, 121, 121, 121, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 156, 164] 164 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 27, 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, 34, 35]) total number of confs: 627 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: REAL250005052034 none CC(CNC(=O)C1CCSC1)NC(=O)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', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 14, 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 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [21, 9, 21, 58, 116, 116, 116, 164, 164, 164, 164, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 58, 58, 116, 164, 164, 164, 164, 164, 164, 164, 9, 1] 164 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 565 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052034 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052034 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052034/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052034 Building REAL250005052035 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052035' /scratch/stefan/7921156/working/building/REAL250005052035 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052035 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052035/0 /scratch/stefan/7921156/working/building/REAL250005052035 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/156 `/scratch/stefan/7921156/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCO1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052035.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052035 none CC(CNC(=O)C1CCO1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 12, 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, 3, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [100, 58, 13, 13, 1, 13, 1, 1, 1, 1, 100, 119, 119, 119, 125, 125, 125, 125, 125, 100, 100, 100, 100, 58, 58, 13, 1, 1, 1, 1, 1, 119, 125] 125 rigid atoms, others: [4, 6, 7, 8, 9, 26, 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, 31, 32]) total number of confs: 486 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: REAL250005052035 none CC(CNC(=O)C1CCO1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 12, 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, 3, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [20, 9, 20, 46, 95, 95, 95, 125, 125, 125, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 46, 46, 95, 125, 125, 125, 125, 125, 9, 1] 125 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: 429 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052035 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052035 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052035/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052035 Building REAL250005052036 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052036' /scratch/stefan/7921156/working/building/REAL250005052036 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052036 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052036/0 /scratch/stefan/7921156/working/building/REAL250005052036 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/157 `/scratch/stefan/7921156/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCN=[N+]=[N-])NC(=O)C1=CC(=O)[N-]O1) `REAL250005052036.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052036 none CC(CNC(=O)CCN=[N+]=[N-])NC(=O)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.2', 'O.2', 'C.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, 5, 8, 8, 8, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 23, 59, 59, 59, 144, 171, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 23, 23, 59, 144, 144, 171, 171, 4, 1] 201 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052036 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052036 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052036/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052036 Building REAL250005052037 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052037' /scratch/stefan/7921156/working/building/REAL250005052037 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052037 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052037/0 /scratch/stefan/7921156/working/building/REAL250005052037 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/158 `/scratch/stefan/7921156/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052037.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052037 none C#CCOCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 153, 113, 64, 64, 64, 20, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 113, 113, 64, 20, 20, 9, 9, 9, 9, 4, 1] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 771 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052037 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052037 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052037/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052037 Building REAL250005052038 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052038' /scratch/stefan/7921156/working/building/REAL250005052038 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052038 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052038/0 /scratch/stefan/7921156/working/building/REAL250005052038 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/159 `/scratch/stefan/7921156/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1=NN=CO1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052038.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052038 none CC(CNC(=O)CC1=NN=CO1)NC(=O)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', 'N.2', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 130, 35, 35, 4, 35, 1, 1, 1, 1, 1, 1, 182, 200, 200, 200, 201, 201, 201, 201, 201, 182, 182, 182, 182, 130, 130, 35, 4, 4, 1, 200, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 30] 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, 31, 32]) total number of confs: 820 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: REAL250005052038 none CC(CNC(=O)CC1=NN=CO1)NC(=O)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', 'N.2', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 10, 25, 69, 69, 69, 161, 201, 201, 201, 201, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 25, 25, 69, 161, 161, 201, 5, 1] 201 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 677 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052038 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052038 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052038/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052038 Building REAL250005052039 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052039' /scratch/stefan/7921156/working/building/REAL250005052039 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052039 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052039/0 /scratch/stefan/7921156/working/building/REAL250005052039 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/160 `/scratch/stefan/7921156/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCCS1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052039.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052039 none CC(CNC(=O)C1CCCS1)NC(=O)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', 'S.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [95, 55, 12, 12, 1, 12, 1, 1, 1, 1, 1, 95, 108, 108, 108, 110, 110, 110, 110, 110, 95, 95, 95, 95, 55, 55, 12, 1, 1, 1, 1, 1, 1, 1, 108, 110] 110 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 27, 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, 34, 35]) total number of confs: 439 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: REAL250005052039 none CC(CNC(=O)C1CCCS1)NC(=O)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', 'S.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 14, 33, 71, 71, 71, 110, 110, 110, 110, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 33, 33, 71, 110, 110, 110, 110, 110, 110, 110, 7, 1] 110 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: 359 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052039 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052039 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052039/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052039 Building REAL250005052040 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052040' /scratch/stefan/7921156/working/building/REAL250005052040 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052040 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052040/0 /scratch/stefan/7921156/working/building/REAL250005052040 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/161 `/scratch/stefan/7921156/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)(C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052040.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052040 none CC(CNC(=O)C(C)(C)O)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 372 conformations in input total number of sets (complete confs): 372 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 39, 83, 83, 83, 124, 124, 124, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 39, 39, 83, 124, 124, 124, 124, 124, 124, 372, 8, 1] 372 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: 861 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052040 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052040 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052040/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052040 Building REAL250005052041 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052041' /scratch/stefan/7921156/working/building/REAL250005052041 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052041 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052041/0 /scratch/stefan/7921156/working/building/REAL250005052041 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/162 `/scratch/stefan/7921156/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052041.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052041 none CC1=CC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 74, 148, 151, 193, 193, 193, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 13, 74, 74, 151, 151, 151, 151, 193, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 833 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: REAL250005052041 none CC1=CC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 117, 117, 117, 55, 21, 8, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 117, 55, 55, 21, 21, 21, 21, 8, 1] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 675 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052041 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052041 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052041/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052041 Building REAL250005052042 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052042' /scratch/stefan/7921156/working/building/REAL250005052042 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052042 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052042/0 /scratch/stefan/7921156/working/building/REAL250005052042 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/163 `/scratch/stefan/7921156/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(=O)N(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052042.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052042 none CC(CNC(=O)C(=O)N(C)C)NC(=O)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.2', 'O.2', 'C.2', 'C.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, 11, 8, 5, 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, 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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [16, 9, 16, 34, 64, 64, 64, 72, 71, 71, 72, 9, 1, 9, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 34, 34, 64, 72, 72, 72, 72, 72, 72, 9, 1] 72 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052042 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052042 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052042/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052042 Building REAL250005052043 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052043' /scratch/stefan/7921156/working/building/REAL250005052043 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052043 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052043/0 /scratch/stefan/7921156/working/building/REAL250005052043 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/164 `/scratch/stefan/7921156/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052043.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052043 none CSC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 169, 169, 107, 107, 107, 50, 17, 7, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 169, 169, 107, 50, 50, 17, 17, 17, 17, 7, 1] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 601 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052043 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052043 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052043/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052043 Building REAL250005052044 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052044' /scratch/stefan/7921156/working/building/REAL250005052044 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052044 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052044/0 /scratch/stefan/7921156/working/building/REAL250005052044 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/165 `/scratch/stefan/7921156/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052044.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052044 none CCC(C)(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [194, 180, 112, 180, 180, 112, 112, 52, 20, 9, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 180, 180, 180, 540, 112, 52, 52, 20, 20, 20, 20, 9, 1] 603 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1407 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052044 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052044 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052044/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052044 Building REAL250005052045 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052045' /scratch/stefan/7921156/working/building/REAL250005052045 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005052045 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052045/0 /scratch/stefan/7921156/working/building/REAL250005052045 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/166 `/scratch/stefan/7921156/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052045.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052045 none CC[N@H+](C)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 26, 27, 27, 24, 24, 24, 13, 7, 3, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 26, 26, 24, 13, 13, 7, 7, 7, 7, 3, 1] 27 rigid atoms, others: [39, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 107 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052045 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052045/1 /scratch/stefan/7921156/working/building/REAL250005052045 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/167 `/scratch/stefan/7921156/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052045.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052045/1/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: REAL250005052045 none CC[N@@H+](C)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 18, 19, 19, 16, 16, 16, 10, 6, 3, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 16, 10, 10, 6, 6, 6, 6, 3, 1] 19 rigid atoms, others: [39, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052045 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `2' /scratch/stefan/7921156/working/building/REAL250005052045/2 /scratch/stefan/7921156/working/building/REAL250005052045 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 2 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/168 `/scratch/stefan/7921156/working/3D/168' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052045.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005052045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052045/2/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: REAL250005052045 none CCN(C)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 182, 187, 142, 142, 142, 60, 22, 7, 22, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 187, 187, 187, 182, 182, 142, 60, 60, 22, 22, 22, 22, 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: 797 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052045 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052045 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052045/0.* 2: /scratch/stefan/7921156/working/building/REAL250005052045/2.* 1: /scratch/stefan/7921156/working/building/REAL250005052045/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052045 Building REAL250005052046 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052046' /scratch/stefan/7921156/working/building/REAL250005052046 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052046 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052046/0 /scratch/stefan/7921156/working/building/REAL250005052046 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/169 `/scratch/stefan/7921156/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052046.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052046 none CCC=CC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 153, 153, 134, 134, 72, 72, 72, 36, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 153, 153, 134, 134, 72, 36, 36, 12, 12, 12, 12, 4, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 795 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052046 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052046 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052046/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052046 Building REAL250005052047 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052047' /scratch/stefan/7921156/working/building/REAL250005052047 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052047 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052047/0 /scratch/stefan/7921156/working/building/REAL250005052047 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/170 `/scratch/stefan/7921156/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[N-]1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052047.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052047 none CC(CNC(=O)C1=CC(=O)N[N-]1)NC(=O)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', 'O.2', 'N.am', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [40, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 42, 54, 54, 54, 54, 54, 54, 54, 54, 42, 42, 42, 42, 25, 25, 8, 1, 1, 54, 54] 54 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) 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: REAL250005052047 none CC(CNC(=O)C1=CC(=O)N[N-]1)NC(=O)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', 'O.2', 'N.am', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 30, 47, 47, 47, 54, 54, 54, 54, 54, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 30, 30, 47, 54, 54, 5, 1] 54 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 184 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052047 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052047 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052047/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052047 Building REAL250005052048 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052048' /scratch/stefan/7921156/working/building/REAL250005052048 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052048 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052048/0 /scratch/stefan/7921156/working/building/REAL250005052048 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/171 `/scratch/stefan/7921156/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)=CN1) `REAL250005052048.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052048 none CC1=CC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 28, 98, 99, 135, 135, 135, 146, 146, 146, 146, 146, 1, 1, 2, 2, 2, 1, 5, 28, 28, 99, 99, 99, 99, 135, 146, 1, 1] 146 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 553 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: REAL250005052048 none CC1=CC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 111, 111, 111, 62, 22, 9, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 146, 146, 111, 62, 62, 22, 22, 22, 22, 9, 1, 146, 146] 146 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: 450 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052048 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052048 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052048/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052048 Building REAL250005052049 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052049' /scratch/stefan/7921156/working/building/REAL250005052049 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052049 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052049/0 /scratch/stefan/7921156/working/building/REAL250005052049 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/172 `/scratch/stefan/7921156/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005052049.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052049 none CC1=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 49, 105, 108, 133, 133, 133, 140, 140, 140, 140, 140, 1, 1, 1, 2, 2, 2, 9, 49, 49, 108, 108, 108, 108, 133, 140, 1, 1, 1, 1, 1, 1] 140 rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 33, 34, 18, 19, 20, 38] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 561 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: REAL250005052049 none CC1=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 90, 90, 90, 40, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 140, 90, 40, 40, 15, 15, 15, 15, 7, 1, 140, 140, 140, 140, 140, 140] 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: 382 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052049 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052049 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052049/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052049 Building REAL250005052050 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052050' /scratch/stefan/7921156/working/building/REAL250005052050 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052050 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052050/0 /scratch/stefan/7921156/working/building/REAL250005052050 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/173 `/scratch/stefan/7921156/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052050.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052050 none C=C1CC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 10, 10, 10, 51, 128, 129, 170, 170, 170, 179, 179, 179, 179, 179, 1, 1, 1, 1, 1, 1, 10, 51, 51, 129, 129, 129, 129, 170, 179, 1, 1] 179 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 19, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052050 none C=C1CC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 108, 108, 108, 58, 21, 10, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 179, 179, 179, 179, 179, 179, 108, 58, 58, 21, 21, 21, 21, 10, 1, 179, 179] 179 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: 617 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052050 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052050 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052050/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052050 Building REAL250005052051 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052051' /scratch/stefan/7921156/working/building/REAL250005052051 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052051 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052051/0 /scratch/stefan/7921156/working/building/REAL250005052051 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/174 `/scratch/stefan/7921156/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)(O)C1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052051.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052051 none CC(CNC(=O)C(C)(O)C1CC1)NC(=O)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, 7, 6, 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 576 conformations in input total number of sets (complete confs): 576 using faster count positions algorithm for large data unique positions, atoms: [168, 114, 37, 37, 10, 37, 1, 10, 10, 1, 1, 1, 168, 190, 190, 190, 192, 192, 192, 192, 192, 168, 168, 168, 168, 114, 114, 37, 10, 10, 10, 30, 1, 1, 1, 1, 1, 190, 192] 576 rigid atoms, others: [32, 33, 34, 35, 36, 6, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 805 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: REAL250005052051 none CC(CNC(=O)C(C)(O)C1CC1)NC(=O)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, 7, 6, 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 576 conformations in input total number of sets (complete confs): 576 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 39, 103, 103, 103, 182, 182, 182, 192, 192, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 39, 39, 103, 182, 182, 182, 546, 192, 192, 192, 192, 192, 7, 1] 576 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: 1302 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052051 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052051 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052051/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052051 Building REAL250005052052 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052052' /scratch/stefan/7921156/working/building/REAL250005052052 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052052 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052052/0 /scratch/stefan/7921156/working/building/REAL250005052052 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/175 `/scratch/stefan/7921156/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005052052.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052052 none CC1=NC=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 49, 50, 71, 71, 71, 77, 77, 77, 77, 77, 1, 2, 2, 2, 1, 5, 21, 21, 50, 50, 50, 50, 71, 77] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 290 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: REAL250005052052 none CC1=NC=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 73, 73, 73, 41, 17, 7, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 73, 41, 41, 17, 17, 17, 17, 7, 1] 77 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 263 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052052 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052052 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052052/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052052 Building REAL250005052053 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052053' /scratch/stefan/7921156/working/building/REAL250005052053 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052053 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052053/0 /scratch/stefan/7921156/working/building/REAL250005052053 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/176 `/scratch/stefan/7921156/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCC1F)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052053.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052053 none CC(CNC(=O)C1CCC1F)NC(=O)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.2', 'O.2', 'C.2', 'C.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, 5, 15, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [141, 63, 12, 12, 1, 12, 1, 1, 1, 1, 1, 143, 167, 167, 167, 172, 172, 172, 172, 172, 143, 143, 143, 143, 63, 63, 12, 1, 1, 1, 1, 1, 1, 167, 172] 172 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 27, 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, 33, 34]) total number of confs: 692 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: REAL250005052053 none CC(CNC(=O)C1CCC1F)NC(=O)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.2', 'O.2', 'C.2', 'C.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, 5, 15, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 23, 60, 112, 112, 112, 172, 172, 172, 172, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 60, 60, 112, 172, 172, 172, 172, 172, 172, 9, 1] 172 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 576 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052053 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052053 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052053/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052053 Building REAL250005052054 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052054' /scratch/stefan/7921156/working/building/REAL250005052054 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052054 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052054/0 /scratch/stefan/7921156/working/building/REAL250005052054 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/177 `/scratch/stefan/7921156/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CN=CN1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052054.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052054 none CC(CNC(=O)C1=CN=CN1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 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: [65, 36, 7, 7, 1, 7, 1, 1, 1, 1, 1, 66, 79, 79, 79, 82, 82, 82, 82, 82, 66, 66, 66, 66, 36, 36, 7, 1, 1, 1, 79, 82] 82 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 329 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: REAL250005052054 none CC(CNC(=O)C1=CN=CN1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 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: [18, 9, 18, 40, 65, 65, 65, 82, 82, 82, 82, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 40, 40, 65, 82, 82, 82, 9, 1] 82 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 262 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052054 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052054 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052054/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052054 Building REAL250005052055 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052055' /scratch/stefan/7921156/working/building/REAL250005052055 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052055 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052055/0 /scratch/stefan/7921156/working/building/REAL250005052055 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/178 `/scratch/stefan/7921156/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005052055.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052055 none CC1=NOC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 27, 59, 60, 82, 82, 82, 88, 88, 88, 88, 88, 1, 2, 2, 2, 5, 26, 26, 60, 60, 60, 60, 82, 88] 88 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 329 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: REAL250005052055 none CC1=NOC(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 73, 73, 73, 45, 20, 8, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 73, 45, 45, 20, 20, 20, 20, 8, 1] 88 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: 298 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052055 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052055 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052055/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052055 Building REAL250005052056 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052056' /scratch/stefan/7921156/working/building/REAL250005052056 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052056 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052056/0 /scratch/stefan/7921156/working/building/REAL250005052056 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/179 `/scratch/stefan/7921156/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC2CC2C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052056.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052056 none CC(CNC(=O)C1CC2CC2C1)NC(=O)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, 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: [145, 57, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 146, 192, 192, 192, 201, 201, 201, 201, 201, 146, 146, 146, 146, 57, 57, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 192, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 36, 28, 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, 37, 38]) total number of confs: 773 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: REAL250005052056 none CC(CNC(=O)C1CC2CC2C1)NC(=O)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, 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: [18, 7, 18, 51, 117, 117, 117, 201, 201, 201, 201, 201, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 51, 51, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201, 8, 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: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052056 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052056 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052056/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052056 Building REAL250005052057 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052057' /scratch/stefan/7921156/working/building/REAL250005052057 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052057 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052057/0 /scratch/stefan/7921156/working/building/REAL250005052057 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/180 `/scratch/stefan/7921156/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCSC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052057.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052057 none CC(CNC(=O)C1=CCSC1)NC(=O)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', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 14, 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, 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 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [129, 61, 13, 13, 1, 13, 1, 1, 1, 1, 1, 129, 160, 160, 160, 168, 168, 168, 168, 168, 129, 129, 129, 129, 61, 61, 13, 1, 1, 1, 1, 1, 160, 168] 168 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27, 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, 32, 33]) total number of confs: 661 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: REAL250005052057 none CC(CNC(=O)C1=CCSC1)NC(=O)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', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 14, 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, 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 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 60, 121, 121, 121, 168, 168, 168, 168, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 60, 60, 121, 168, 168, 168, 168, 168, 8, 1] 168 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 503 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052057 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052057 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052057/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052057 Building REAL250005052058 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052058' /scratch/stefan/7921156/working/building/REAL250005052058 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052058 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052058/0 /scratch/stefan/7921156/working/building/REAL250005052058 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/181 `/scratch/stefan/7921156/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052058.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052058 none CCCC(O)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 151, 101, 151, 59, 59, 59, 23, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 196, 196, 151, 453, 101, 101, 59, 23, 23, 10, 10, 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: 1363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052058 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052058 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052058/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052058 Building REAL250005052059 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052059' /scratch/stefan/7921156/working/building/REAL250005052059 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052059 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052059/0 /scratch/stefan/7921156/working/building/REAL250005052059 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/182 `/scratch/stefan/7921156/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(Cl)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052059.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052059 none CC(CNC(=O)C1(Cl)CC1)NC(=O)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', 'Cl', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 16, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [132, 64, 13, 13, 1, 13, 1, 1, 1, 1, 132, 153, 153, 153, 158, 158, 158, 158, 158, 132, 132, 132, 132, 64, 64, 13, 1, 1, 1, 1, 153, 158] 158 rigid atoms, others: [4, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 622 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: REAL250005052059 none CC(CNC(=O)C1(Cl)CC1)NC(=O)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', 'Cl', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 16, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 22, 48, 104, 104, 104, 158, 158, 158, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 48, 48, 104, 158, 158, 158, 158, 10, 1] 158 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: 536 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052059 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052059 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052059/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052059 Building REAL250005052060 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052060' /scratch/stefan/7921156/working/building/REAL250005052060 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052060 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052060/0 /scratch/stefan/7921156/working/building/REAL250005052060 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/183 `/scratch/stefan/7921156/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCCO1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052060.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052060 none CC(CNC(=O)C1=CCCO1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 12, 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, 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 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [103, 51, 12, 12, 1, 12, 1, 1, 1, 1, 1, 104, 131, 131, 131, 137, 137, 137, 137, 137, 104, 104, 104, 104, 50, 50, 12, 1, 1, 1, 1, 1, 131, 137] 137 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27, 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, 32, 33]) total number of confs: 540 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052060 none CC(CNC(=O)C1=CCCO1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 12, 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, 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 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 57, 106, 106, 106, 137, 137, 137, 137, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 57, 57, 106, 137, 137, 137, 137, 137, 8, 1] 137 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: 432 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052060 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052060 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052060/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052060 Building REAL250005052061 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052061' /scratch/stefan/7921156/working/building/REAL250005052061 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052061 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052061/0 /scratch/stefan/7921156/working/building/REAL250005052061 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/184 `/scratch/stefan/7921156/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CC[NH+](C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052061.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052061 none CC(CNC(=O)C=CC[NH+](C)C)NC(=O)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', 'N.4', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 9, 6, 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, 1, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 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: [12, 9, 12, 13, 21, 21, 21, 26, 26, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 13, 13, 21, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 1] 26 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052061 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052061 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052061/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052061 Building REAL250005052062 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052062' /scratch/stefan/7921156/working/building/REAL250005052062 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052062 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052062/0 /scratch/stefan/7921156/working/building/REAL250005052062 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/185 `/scratch/stefan/7921156/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052062.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052062 none CCC[C@H](O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 195, 139, 107, 139, 139, 107, 107, 45, 17, 6, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 196, 196, 417, 107, 45, 45, 17, 17, 17, 17, 6, 1] 603 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1286 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052062 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052062 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052062/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052062 Building REAL250005052063 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052063' /scratch/stefan/7921156/working/building/REAL250005052063 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052063 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052063/0 /scratch/stefan/7921156/working/building/REAL250005052063 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/186 `/scratch/stefan/7921156/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(OC)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052063.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052063 none CCC(C)(OC)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 183, 108, 183, 182, 192, 108, 108, 42, 15, 4, 15, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 183, 183, 183, 192, 192, 192, 108, 42, 42, 15, 15, 15, 15, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 916 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052063 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052063 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052063/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052063 Building REAL250005052064 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052064' /scratch/stefan/7921156/working/building/REAL250005052064 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052064 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052064/0 /scratch/stefan/7921156/working/building/REAL250005052064 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/187 `/scratch/stefan/7921156/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052064.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052064 none CC(C)[C@H](O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [200, 184, 201, 130, 184, 184, 130, 130, 53, 20, 8, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 552, 130, 53, 53, 20, 20, 20, 20, 8, 1] 603 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1345 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052064 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052064 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052064/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052064 Building REAL250005052065 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052065' /scratch/stefan/7921156/working/building/REAL250005052065 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052065 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052065/0 /scratch/stefan/7921156/working/building/REAL250005052065 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/188 `/scratch/stefan/7921156/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CO)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052065.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052065 none CC(C)C(CO)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 573 conformations in input total number of sets (complete confs): 573 using faster count positions algorithm for large data unique positions, atoms: [179, 149, 176, 74, 149, 187, 74, 74, 26, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 179, 179, 179, 179, 179, 179, 179, 149, 187, 187, 561, 74, 26, 26, 11, 11, 11, 11, 4, 1] 573 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1527 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052065 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052065 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052065/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052065 Building REAL250005052066 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052066' /scratch/stefan/7921156/working/building/REAL250005052066 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052066 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052066/0 /scratch/stefan/7921156/working/building/REAL250005052066 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/189 `/scratch/stefan/7921156/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052066.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052066 none CCOC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 147, 147, 73, 73, 73, 33, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 147, 147, 73, 33, 33, 10, 10, 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: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052066 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052066 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052066/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052066 Building REAL250005052067 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052067' /scratch/stefan/7921156/working/building/REAL250005052067 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005052067 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052067/0 /scratch/stefan/7921156/working/building/REAL250005052067 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/190 `/scratch/stefan/7921156/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052067.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052067 none CCN1CCC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 35, 99, 102, 149, 149, 149, 171, 171, 171, 171, 171, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 9, 35, 35, 102, 102, 102, 102, 149, 171] 185 rigid atoms, others: [1, 2, 3, 4, 5, 6, 26, 27, 28, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 623 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: REAL250005052067 none CCN1CCC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [185, 171, 171, 171, 171, 149, 149, 149, 78, 27, 10, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 185, 185, 185, 185, 185, 171, 171, 171, 171, 171, 149, 78, 78, 27, 27, 27, 27, 10, 1] 185 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: 674 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052067 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052067/1 /scratch/stefan/7921156/working/building/REAL250005052067 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/191 `/scratch/stefan/7921156/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+]1CCC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052067.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052067/1/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: REAL250005052067 none CC[N@@H+]1CCC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 27, 27, 29, 29, 29, 36, 36, 36, 36, 36, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 6, 20, 20, 27, 27, 27, 27, 29, 36] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 27, 28, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 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: REAL250005052067 none CC[N@@H+]1CCC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 36, 36, 36, 36, 34, 34, 34, 22, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 36, 36, 36, 36, 36, 34, 22, 22, 15, 15, 15, 15, 7, 1] 37 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: 136 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052067 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `2' /scratch/stefan/7921156/working/building/REAL250005052067/2 /scratch/stefan/7921156/working/building/REAL250005052067 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 2 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/192 `/scratch/stefan/7921156/working/3D/192' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+]1CCC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052067.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005052067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052067/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052067 none CC[N@H+]1CCC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 20, 25, 25, 26, 26, 26, 36, 36, 36, 36, 36, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 11, 20, 20, 25, 25, 25, 25, 26, 36] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 27, 28, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 130 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: REAL250005052067 none CC[N@H+]1CCC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 36, 36, 36, 36, 28, 28, 28, 14, 10, 8, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 36, 36, 36, 36, 36, 28, 14, 14, 10, 10, 10, 10, 9, 1] 37 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: 131 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052067 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052067 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052067/0.* 2: /scratch/stefan/7921156/working/building/REAL250005052067/2.* 1: /scratch/stefan/7921156/working/building/REAL250005052067/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052067 Building REAL250005052068 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052068' /scratch/stefan/7921156/working/building/REAL250005052068 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052068 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052068/0 /scratch/stefan/7921156/working/building/REAL250005052068 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/193 `/scratch/stefan/7921156/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCCC1O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052068.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052068 none CC(CNC(=O)C1CCCC1O)NC(=O)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', '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, 8, 1, 11, 5, 5, 5, 5, 5, 12, 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, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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] 1 hydrogens need rotated 393 conformations in input total number of sets (complete confs): 393 using faster count positions algorithm for large data unique positions, atoms: [95, 41, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 95, 125, 125, 125, 131, 131, 131, 131, 131, 95, 95, 95, 95, 41, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 125, 131] 393 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 28, 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, 36, 37, 38]) total number of confs: 524 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052068 none CC(CNC(=O)C1CCCC1O)NC(=O)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', '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, 8, 1, 11, 5, 5, 5, 5, 5, 12, 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, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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] 1 hydrogens need rotated 393 conformations in input total number of sets (complete confs): 393 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 57, 98, 98, 98, 131, 131, 131, 131, 131, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 57, 57, 98, 131, 131, 131, 131, 131, 131, 131, 131, 393, 8, 1] 393 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: 847 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052068 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052068 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052068/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052068 Building REAL250005052069 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052069' /scratch/stefan/7921156/working/building/REAL250005052069 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052069 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052069/0 /scratch/stefan/7921156/working/building/REAL250005052069 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/194 `/scratch/stefan/7921156/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H](C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052069.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052069 none 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', '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'] dock atom type numbers: [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, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 369 conformations in input total number of sets (complete confs): 369 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 19, 46, 89, 89, 89, 123, 123, 123, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 46, 46, 89, 123, 123, 123, 369, 9, 1] 369 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 863 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052069 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052069 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052069/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052069 Building REAL250005052070 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052070' /scratch/stefan/7921156/working/building/REAL250005052070 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052070 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052070/0 /scratch/stefan/7921156/working/building/REAL250005052070 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/195 `/scratch/stefan/7921156/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=C(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052070.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052070 none CCC(C)=C(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 103, 143, 103, 103, 46, 16, 7, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 143, 143, 143, 143, 143, 143, 103, 46, 46, 16, 16, 16, 16, 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: 832 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052070 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052070 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052070/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052070 Building REAL250005052071 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052071' /scratch/stefan/7921156/working/building/REAL250005052071 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052071 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052071/0 /scratch/stefan/7921156/working/building/REAL250005052071 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/196 `/scratch/stefan/7921156/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005052071.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052071 none COC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 8, 8, 8, 43, 134, 137, 186, 186, 186, 201, 201, 201, 201, 201, 1, 1, 1, 6, 6, 6, 8, 43, 43, 137, 137, 137, 137, 186, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 36, 37, 35, 33, 34, 18, 19, 20, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 768 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: REAL250005052071 none COC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 149, 149, 70, 24, 10, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 149, 70, 70, 24, 24, 24, 24, 10, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 675 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052071 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052071 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052071/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052071 Building REAL250005052072 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052072' /scratch/stefan/7921156/working/building/REAL250005052072 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052072 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052072/0 /scratch/stefan/7921156/working/building/REAL250005052072 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/197 `/scratch/stefan/7921156/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCC(C)(C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052072.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052072 none CC(CNC(=O)CCC(C)(C)O)NC(=O)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', '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, 8, 1, 11, 5, 5, 5, 5, 5, 12, 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, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 12, 31, 78, 78, 78, 170, 170, 200, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 31, 31, 78, 170, 170, 170, 170, 200, 201, 201, 201, 201, 201, 603, 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: 1428 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052072 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052072 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052072/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052072 Building REAL250005052073 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052073' /scratch/stefan/7921156/working/building/REAL250005052073 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052073 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052073/0 /scratch/stefan/7921156/working/building/REAL250005052073 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/198 `/scratch/stefan/7921156/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CSN=C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052073.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052073 none CC(CNC(=O)C1=CSN=C1)NC(=O)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', 'S.3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 14, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [86, 28, 5, 5, 1, 5, 1, 1, 1, 1, 1, 86, 109, 109, 109, 113, 113, 113, 113, 113, 86, 86, 86, 86, 28, 28, 5, 1, 1, 109, 113] 113 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 436 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: REAL250005052073 none CC(CNC(=O)C1=CSN=C1)NC(=O)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', 'S.3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 14, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 49, 90, 90, 90, 113, 113, 113, 113, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 49, 49, 90, 113, 113, 8, 1] 113 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 371 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052073 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052073 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052073/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052073 Building REAL250005052074 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052074' /scratch/stefan/7921156/working/building/REAL250005052074 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052074 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052074/0 /scratch/stefan/7921156/working/building/REAL250005052074 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/199 `/scratch/stefan/7921156/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(C)CC(C)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052074.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052074 none CC(CNC(=O)C1(C)CC(C)C1)NC(=O)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: [141, 43, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 143, 193, 193, 193, 201, 201, 201, 201, 201, 143, 143, 143, 143, 43, 43, 6, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 193, 201] 201 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 11, 38, 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, 30, 34, 35, 36, 39, 40]) total number of confs: 781 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: REAL250005052074 none CC(CNC(=O)C1(C)CC(C)C1)NC(=O)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: [21, 8, 21, 54, 93, 93, 93, 201, 201, 201, 201, 201, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 54, 54, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 661 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052074 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052074 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052074/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052074 Building REAL250005052075 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052075' /scratch/stefan/7921156/working/building/REAL250005052075 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052075 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052075/0 /scratch/stefan/7921156/working/building/REAL250005052075 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/200 `/scratch/stefan/7921156/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052075.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052075 none CNC(=O)CCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 201, 148, 73, 73, 73, 32, 14, 9, 14, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 170, 170, 148, 148, 73, 32, 32, 14, 14, 14, 14, 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: 800 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052075 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052075 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052075/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052075 Building REAL250005052076 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052076' /scratch/stefan/7921156/working/building/REAL250005052076 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052076 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052076/0 /scratch/stefan/7921156/working/building/REAL250005052076 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/201 `/scratch/stefan/7921156/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCCCF)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052076.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052076 none CC(CNC(=O)CCCCF)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.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, 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: [9, 4, 9, 23, 56, 56, 56, 160, 173, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 23, 23, 56, 160, 160, 195, 195, 199, 200, 201, 201, 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: 949 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052076 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052076 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052076/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052076 Building REAL250005052077 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052077' /scratch/stefan/7921156/working/building/REAL250005052077 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052077 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052077/0 /scratch/stefan/7921156/working/building/REAL250005052077 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/202 `/scratch/stefan/7921156/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CCO)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052077.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052077 none CC(CNC(=O)C=CCO)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 52, 111, 111, 111, 185, 185, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 52, 52, 111, 185, 185, 201, 201, 603, 6, 1] 603 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 1322 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052077 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052077 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052077/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052077 Building REAL250005052078 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052078' /scratch/stefan/7921156/working/building/REAL250005052078 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052078 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052078/0 /scratch/stefan/7921156/working/building/REAL250005052078 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/203 `/scratch/stefan/7921156/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1=CN=CO1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052078.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052078 none CC(CNC(=O)CC1=CN=CO1)NC(=O)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', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 12, 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, 7, 3, 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: [181, 130, 34, 34, 5, 34, 1, 1, 1, 1, 1, 1, 181, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 181, 130, 130, 34, 5, 5, 1, 1, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 30, 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, 32, 33]) total number of confs: 826 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: REAL250005052078 none CC(CNC(=O)CC1=CN=CO1)NC(=O)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', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 12, 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, 7, 3, 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: [10, 4, 10, 26, 61, 61, 61, 131, 201, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 26, 26, 61, 131, 131, 201, 201, 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: 624 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052078 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052078 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052078/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052078 Building REAL250005052079 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052079' /scratch/stefan/7921156/working/building/REAL250005052079 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052079 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052079/0 /scratch/stefan/7921156/working/building/REAL250005052079 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/204 `/scratch/stefan/7921156/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052079.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052079 none COC(C)(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 196, 139, 197, 197, 139, 139, 63, 26, 9, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 199, 199, 199, 197, 197, 197, 197, 197, 197, 139, 63, 63, 26, 26, 26, 26, 9, 1] 199 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: 753 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052079 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052079 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052079/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052079 Building REAL250005052080 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052080' /scratch/stefan/7921156/working/building/REAL250005052080 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052080 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052080/0 /scratch/stefan/7921156/working/building/REAL250005052080 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/205 `/scratch/stefan/7921156/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)(C)[NH+](C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052080.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052080 none CC(CNC(=O)C(C)(C)[NH+](C)C)NC(=O)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.4', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 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, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 11, 16, 16, 16, 20, 20, 20, 20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 11, 11, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1] 20 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: 80 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052080 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052080 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052080/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052080 Building REAL250005052081 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052081' /scratch/stefan/7921156/working/building/REAL250005052081 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052081 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052081/0 /scratch/stefan/7921156/working/building/REAL250005052081 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/206 `/scratch/stefan/7921156/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(F)(F)CO)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052081.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052081 none CC(CNC(=O)C(F)(F)CO)NC(=O)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', 'F', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 15, 15, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 1 hydrogens need rotated 555 conformations in input total number of sets (complete confs): 555 using faster count positions algorithm for large data unique positions, atoms: [17, 10, 17, 35, 94, 94, 94, 181, 181, 181, 185, 10, 1, 10, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 35, 35, 94, 185, 185, 555, 10, 1] 555 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 1272 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052081 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052081 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052081/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052081 Building REAL250005052082 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052082' /scratch/stefan/7921156/working/building/REAL250005052082 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052082 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052082/0 /scratch/stefan/7921156/working/building/REAL250005052082 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/207 `/scratch/stefan/7921156/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCCCO)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052082.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052082 none CC(CNC(=O)CCCCO)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 20, 42, 42, 42, 131, 159, 189, 196, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 42, 131, 131, 175, 175, 192, 192, 201, 201, 588, 4, 1] 603 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1572 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052082 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052082 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052082/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052082 Building REAL250005052083 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052083' /scratch/stefan/7921156/working/building/REAL250005052083 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052083 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052083/0 /scratch/stefan/7921156/working/building/REAL250005052083 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/208 `/scratch/stefan/7921156/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)C=NO1) `REAL250005052083.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052083 none CC1=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 10, 10, 10, 52, 109, 110, 131, 131, 131, 136, 136, 136, 136, 136, 1, 1, 1, 2, 2, 2, 10, 52, 52, 110, 110, 110, 110, 131, 136, 1] 136 rigid atoms, others: [0, 1, 2, 3, 33, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 556 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: REAL250005052083 none CC1=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 96, 96, 96, 45, 19, 9, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 136, 136, 96, 45, 45, 19, 19, 19, 19, 9, 1, 136] 136 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 389 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052083 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052083 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052083/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052083 Building REAL250005052084 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052084' /scratch/stefan/7921156/working/building/REAL250005052084 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052084 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052084/0 /scratch/stefan/7921156/working/building/REAL250005052084 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/209 `/scratch/stefan/7921156/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CNC(=O)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052084.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052084 none CC(CNC(=O)C1CNC(=O)C1)NC(=O)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.am', 'C.2', '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, 5, 5, 8, 1, 11, 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, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [130, 53, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 130, 164, 164, 164, 172, 172, 172, 172, 172, 130, 130, 130, 130, 53, 53, 10, 1, 1, 1, 1, 1, 1, 164, 172] 172 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 28, 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, 34, 35]) total number of confs: 665 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: REAL250005052084 none CC(CNC(=O)C1CNC(=O)C1)NC(=O)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.am', 'C.2', '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, 5, 5, 8, 1, 11, 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, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 9, 20, 55, 119, 119, 119, 172, 172, 172, 172, 172, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 55, 55, 119, 172, 172, 172, 172, 172, 172, 9, 1] 172 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: 583 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052084 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052084 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052084/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052084 Building REAL250005052085 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052085' /scratch/stefan/7921156/working/building/REAL250005052085 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052085 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052085/0 /scratch/stefan/7921156/working/building/REAL250005052085 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/210 `/scratch/stefan/7921156/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1CNC(=O)N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052085.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052085 none CC(CNC(=O)[C@@H]1CNC(=O)N1)NC(=O)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.am', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [115, 62, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 115, 136, 136, 136, 141, 141, 141, 141, 141, 115, 115, 115, 115, 62, 62, 12, 1, 1, 1, 1, 136, 141] 141 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 557 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: REAL250005052085 none CC(CNC(=O)[C@@H]1CNC(=O)N1)NC(=O)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.am', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 17, 44, 96, 96, 96, 141, 141, 141, 141, 141, 141, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 44, 44, 96, 141, 141, 141, 141, 8, 1] 141 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 470 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052085 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052085 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052085/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052085 Building REAL250005052086 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052086' /scratch/stefan/7921156/working/building/REAL250005052086 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052086 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052086/0 /scratch/stefan/7921156/working/building/REAL250005052086 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/211 `/scratch/stefan/7921156/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CN=CS1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052086.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052086 none CC(CNC(=O)C1=CN=CS1)NC(=O)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', 'S.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [77, 44, 9, 9, 1, 9, 1, 1, 1, 1, 1, 78, 102, 102, 102, 104, 104, 104, 104, 104, 78, 78, 78, 78, 43, 43, 10, 1, 1, 102, 104] 104 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 415 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: REAL250005052086 none CC(CNC(=O)C1=CN=CS1)NC(=O)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', 'S.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 18, 49, 77, 77, 77, 104, 104, 104, 104, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 49, 49, 77, 104, 104, 7, 1] 104 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 339 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052086 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052086 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052086/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052086 Building REAL250005052087 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052087' /scratch/stefan/7921156/working/building/REAL250005052087 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052087 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052087/0 /scratch/stefan/7921156/working/building/REAL250005052087 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/212 `/scratch/stefan/7921156/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005052087.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052087 none CC1=CC=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 32, 75, 76, 94, 94, 94, 100, 100, 100, 100, 100, 1, 2, 2, 2, 1, 1, 7, 32, 32, 76, 76, 76, 76, 94, 100, 1] 100 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 396 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: REAL250005052087 none CC1=CC=C(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 85, 85, 85, 51, 20, 9, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 100, 85, 51, 51, 20, 20, 20, 20, 9, 1, 100] 100 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 334 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052087 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052087 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052087/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052087 Building REAL250005052088 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052088' /scratch/stefan/7921156/working/building/REAL250005052088 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052088 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052088/0 /scratch/stefan/7921156/working/building/REAL250005052088 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/213 `/scratch/stefan/7921156/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(CO)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052088.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052088 none CC(CNC(=O)C1(CO)CC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 4, 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: [113, 40, 7, 7, 1, 7, 1, 1, 8, 1, 1, 113, 181, 181, 181, 188, 188, 188, 188, 188, 113, 113, 113, 113, 40, 40, 7, 8, 8, 24, 1, 1, 1, 1, 181, 188] 603 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]) total number of confs: 739 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052088 none CC(CNC(=O)C1(CO)CC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 4, 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: [14, 4, 14, 40, 97, 97, 97, 188, 201, 188, 188, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 40, 40, 97, 201, 201, 603, 188, 188, 188, 188, 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: 1275 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052088 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052088 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052088/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052088 Building REAL250005052089 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052089' /scratch/stefan/7921156/working/building/REAL250005052089 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052089 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052089/0 /scratch/stefan/7921156/working/building/REAL250005052089 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/214 `/scratch/stefan/7921156/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(CC(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005052089.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052089 none COC1(CC(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 9, 54, 54, 54, 122, 158, 158, 190, 190, 190, 192, 192, 192, 192, 192, 1, 1, 6, 6, 6, 9, 9, 54, 122, 122, 158, 158, 158, 158, 190, 192, 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: 760 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052089 none COC1(CC(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 141, 57, 57, 57, 33, 13, 5, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 192, 192, 201, 201, 201, 141, 141, 57, 33, 33, 13, 13, 13, 13, 5, 1, 192, 192, 192, 192] 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: 763 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052089 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052089 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052089/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052089 Building REAL250005052090 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052090' /scratch/stefan/7921156/working/building/REAL250005052090 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052090 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052090/0 /scratch/stefan/7921156/working/building/REAL250005052090 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/215 `/scratch/stefan/7921156/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052090.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052090 none CC[C@H](C)[C@H](O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 193, 149, 193, 193, 114, 149, 149, 114, 114, 49, 16, 5, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 193, 447, 114, 49, 49, 16, 16, 16, 16, 5, 1] 603 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1288 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052090 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052090 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052090/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052090 Building REAL250005052091 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052091' /scratch/stefan/7921156/working/building/REAL250005052091 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052091 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052091/0 /scratch/stefan/7921156/working/building/REAL250005052091 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/216 `/scratch/stefan/7921156/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@]12C[C@H]1[C@H](O)C2)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052091.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052091 none CC(CNC(=O)[C@]12C[C@H]1[C@H](O)C2)NC(=O)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', 'H', 'C.3', 'H', '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, 5, 5, 7, 5, 7, 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, 7, 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] 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: [138, 42, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 140, 197, 198, 197, 201, 201, 201, 201, 201, 140, 140, 140, 140, 42, 42, 7, 1, 1, 6, 1, 1, 198, 201] 603 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36]) total number of confs: 787 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: REAL250005052091 none CC(CNC(=O)[C@]12C[C@H]1[C@H](O)C2)NC(=O)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', 'H', 'C.3', 'H', '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, 5, 5, 7, 5, 7, 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, 7, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 18, 59, 121, 121, 121, 201, 201, 201, 201, 201, 201, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 59, 59, 121, 201, 201, 603, 201, 201, 7, 1] 603 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1151 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052091 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052091 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052091/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052091 Building REAL250005052092 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052092' /scratch/stefan/7921156/working/building/REAL250005052092 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052092 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052092/0 /scratch/stefan/7921156/working/building/REAL250005052092 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/217 `/scratch/stefan/7921156/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052092.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052092 none COC(F)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 124, 199, 124, 124, 54, 18, 7, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 124, 54, 54, 18, 18, 18, 18, 7, 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: 786 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052092 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052092 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052092/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052092 Building REAL250005052093 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052093' /scratch/stefan/7921156/working/building/REAL250005052093 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052093 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052093/0 /scratch/stefan/7921156/working/building/REAL250005052093 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/218 `/scratch/stefan/7921156/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C12CC1CC2)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052093.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052093 none CC(CNC(=O)C12CC1CC2)NC(=O)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'] 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 42, 7, 7, 1, 7, 1, 1, 1, 1, 1, 137, 193, 193, 193, 201, 201, 201, 201, 201, 137, 137, 137, 137, 42, 42, 7, 1, 1, 1, 1, 1, 1, 1, 193, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 27, 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, 34, 35]) total number of confs: 775 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: REAL250005052093 none CC(CNC(=O)C12CC1CC2)NC(=O)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'] 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 20, 55, 97, 97, 97, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 55, 55, 97, 201, 201, 201, 201, 201, 201, 201, 7, 1] 201 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 501 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052093 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052093 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052093/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052093 Building REAL250005052094 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052094' /scratch/stefan/7921156/working/building/REAL250005052094 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052094 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052094/0 /scratch/stefan/7921156/working/building/REAL250005052094 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/219 `/scratch/stefan/7921156/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052094.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052094 none CCCC(C)=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 125, 125, 125, 70, 70, 70, 26, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 195, 195, 125, 125, 125, 125, 70, 26, 26, 9, 9, 9, 9, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 825 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052094 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052094 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052094/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052094 Building REAL250005052095 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052095' /scratch/stefan/7921156/working/building/REAL250005052095 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052095 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052095/0 /scratch/stefan/7921156/working/building/REAL250005052095 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/220 `/scratch/stefan/7921156/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@H](C)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052095.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052095 none C=C[C@H](C)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 201, 201, 75, 75, 75, 34, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 149, 149, 75, 34, 34, 12, 12, 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: 866 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052095 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052095 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052095/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052095 Building REAL250005052096 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052096' /scratch/stefan/7921156/working/building/REAL250005052096 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052096 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052096/0 /scratch/stefan/7921156/working/building/REAL250005052096 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/221 `/scratch/stefan/7921156/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CC1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052096.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052096 none CC(CNC(=O)C=CC1CC1)NC(=O)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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 123, 40, 40, 9, 39, 9, 1, 1, 1, 1, 177, 201, 201, 201, 201, 201, 201, 201, 201, 176, 177, 177, 177, 123, 123, 40, 9, 9, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 812 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: REAL250005052096 none CC(CNC(=O)C=CC1CC1)NC(=O)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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 45, 94, 94, 94, 169, 169, 201, 201, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 45, 45, 94, 169, 169, 201, 201, 201, 201, 201, 5, 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: 670 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052096 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052096 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052096/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052096 Building REAL250005052097 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052097' /scratch/stefan/7921156/working/building/REAL250005052097 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052097 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052097/0 /scratch/stefan/7921156/working/building/REAL250005052097 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/222 `/scratch/stefan/7921156/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(CC)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052097.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052097 none CC=C(CC)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 88, 160, 201, 88, 88, 39, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 201, 201, 201, 201, 201, 88, 39, 39, 13, 13, 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: 764 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052097 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052097 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052097/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052097 Building REAL250005052098 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052098' /scratch/stefan/7921156/working/building/REAL250005052098 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052098 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052098/0 /scratch/stefan/7921156/working/building/REAL250005052098 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/223 `/scratch/stefan/7921156/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC12CC(C1)C2)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052098.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052098 none CC(CNC(=O)CC12CC(C1)C2)NC(=O)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, 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: [171, 122, 43, 43, 9, 43, 1, 1, 1, 1, 1, 1, 171, 198, 198, 198, 201, 201, 201, 201, 201, 171, 171, 171, 171, 122, 122, 43, 9, 9, 1, 1, 1, 1, 1, 1, 1, 198, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 30, 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, 37, 38]) total number of confs: 798 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: REAL250005052098 none CC(CNC(=O)CC12CC(C1)C2)NC(=O)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, 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: [19, 7, 19, 56, 113, 113, 113, 201, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 56, 56, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 7, 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: 793 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052098 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052098 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052098/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052098 Building REAL250005052099 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052099' /scratch/stefan/7921156/working/building/REAL250005052099 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052099 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052099/0 /scratch/stefan/7921156/working/building/REAL250005052099 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/224 `/scratch/stefan/7921156/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1)C(C)O) `REAL250005052099.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052099 none CCC(C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1)C(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 360 conformations in input total number of sets (complete confs): 360 using faster count positions algorithm for large data unique positions, atoms: [97, 89, 54, 54, 54, 24, 12, 6, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 89, 119, 119, 98, 98, 98, 98, 98, 89, 54, 24, 24, 12, 12, 12, 12, 6, 1, 119, 119, 119, 119, 357] 360 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 947 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052099 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052099 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052099/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052099 Building REAL250005052100 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052100' /scratch/stefan/7921156/working/building/REAL250005052100 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052100 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052100/0 /scratch/stefan/7921156/working/building/REAL250005052100 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/225 `/scratch/stefan/7921156/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052100.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052100 none C=CC(C)(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 591 conformations in input total number of sets (complete confs): 591 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 156, 197, 197, 156, 156, 68, 23, 8, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 197, 591, 156, 68, 68, 23, 23, 23, 23, 8, 1] 591 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: 1339 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052100 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052100 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052100/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052100 Building REAL250005052101 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052101' /scratch/stefan/7921156/working/building/REAL250005052101 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052101 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052101/0 /scratch/stefan/7921156/working/building/REAL250005052101 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/226 `/scratch/stefan/7921156/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CO)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052101.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052101 none CCC(C)(CO)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [173, 152, 93, 152, 152, 198, 93, 93, 37, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 181, 152, 152, 152, 198, 198, 594, 93, 37, 37, 14, 14, 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: 1644 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052101 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052101 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052101/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052101 Building REAL250005052102 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052102' /scratch/stefan/7921156/working/building/REAL250005052102 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052102 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052102/0 /scratch/stefan/7921156/working/building/REAL250005052102 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/227 `/scratch/stefan/7921156/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1([NH+](C)C)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052102.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052102 none CC(CNC(=O)C1([NH+](C)C)CC1)NC(=O)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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 4, 4, 1, 4, 1, 1, 4, 4, 4, 1, 1, 21, 23, 23, 23, 25, 25, 25, 25, 25, 21, 21, 21, 21, 14, 14, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 23, 25] 25 rigid atoms, others: [35, 4, 37, 6, 7, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 8, 9, 10, 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: 114 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: REAL250005052102 none CC(CNC(=O)C1([NH+](C)C)CC1)NC(=O)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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 18, 23, 23, 23, 25, 25, 25, 25, 25, 25, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 18, 18, 23, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 7, 1] 25 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 89 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052102 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052102/1 /scratch/stefan/7921156/working/building/REAL250005052102 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/228 `/scratch/stefan/7921156/working/3D/228' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(N(C)C)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052102.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052102/1/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: REAL250005052102 none CC(CNC(=O)C1(N(C)C)CC1)NC(=O)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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [91, 35, 8, 8, 1, 8, 1, 1, 4, 4, 1, 1, 91, 136, 136, 136, 145, 145, 145, 145, 145, 91, 91, 91, 91, 35, 35, 8, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 136, 145] 145 rigid atoms, others: [34, 35, 4, 37, 6, 7, 10, 11, 36] set([0, 1, 2, 3, 5, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 550 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: REAL250005052102 none CC(CNC(=O)C1(N(C)C)CC1)NC(=O)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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [23, 10, 23, 55, 105, 105, 105, 145, 145, 145, 145, 145, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 55, 55, 105, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 10, 1] 145 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: 500 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052102 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052102 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052102/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052102/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052102 Building REAL250005052103 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052103' /scratch/stefan/7921156/working/building/REAL250005052103 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052103 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052103/0 /scratch/stefan/7921156/working/building/REAL250005052103 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/229 `/scratch/stefan/7921156/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C12CC(C1)CO2)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052103.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052103 none CC(CNC(=O)C12CC(C1)CO2)NC(=O)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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [141, 74, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 141, 168, 168, 168, 177, 177, 177, 177, 177, 141, 141, 141, 141, 74, 74, 13, 1, 1, 1, 1, 1, 1, 1, 168, 177] 177 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 28, 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, 35, 36]) total number of confs: 704 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: REAL250005052103 none CC(CNC(=O)C12CC(C1)CO2)NC(=O)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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 9, 20, 48, 104, 104, 104, 177, 177, 177, 177, 177, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 48, 48, 104, 177, 177, 177, 177, 177, 177, 177, 9, 1] 177 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: 473 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052103 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052103 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052103/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052103 Building REAL250005052104 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052104' /scratch/stefan/7921156/working/building/REAL250005052104 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052104 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052104/0 /scratch/stefan/7921156/working/building/REAL250005052104 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/230 `/scratch/stefan/7921156/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H](C)C(C)(C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052104.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052104 none CC(CNC(=O)[C@H](C)C(C)(C)O)NC(=O)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', '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, 8, 1, 11, 5, 7, 5, 5, 5, 5, 12, 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, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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 447 conformations in input total number of sets (complete confs): 447 using faster count positions algorithm for large data unique positions, atoms: [22, 8, 22, 59, 111, 111, 111, 140, 140, 140, 149, 140, 149, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 59, 59, 111, 140, 140, 140, 149, 149, 149, 149, 149, 149, 447, 8, 1] 447 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: 1092 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052104 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052104 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052104/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052104 Building REAL250005052105 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052105' /scratch/stefan/7921156/working/building/REAL250005052105 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052105 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052105/0 /scratch/stefan/7921156/working/building/REAL250005052105 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/231 `/scratch/stefan/7921156/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C12CC(C1)OC2)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052105.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052105 none CC(CNC(=O)C12CC(C1)OC2)NC(=O)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'] 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, 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: [137, 40, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 139, 189, 189, 189, 201, 201, 201, 201, 201, 139, 139, 139, 139, 40, 40, 7, 1, 1, 1, 1, 1, 1, 1, 189, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 28, 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, 35, 36]) total number of confs: 761 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: REAL250005052105 none CC(CNC(=O)C12CC(C1)OC2)NC(=O)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'] 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, 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: [18, 7, 18, 49, 79, 79, 79, 201, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 49, 49, 79, 201, 201, 201, 201, 201, 201, 201, 7, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 456 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052105 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052105 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052105/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052105 Building REAL250005052106 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052106' /scratch/stefan/7921156/working/building/REAL250005052106 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052106 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052106/0 /scratch/stefan/7921156/working/building/REAL250005052106 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/232 `/scratch/stefan/7921156/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C1CC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052106.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052106 none CC(O)C1CC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 6, 6, 6, 27, 41, 41, 48, 48, 48, 49, 49, 49, 49, 49, 3, 3, 3, 2, 6, 1, 1, 1, 1, 6, 27, 27, 41, 41, 41, 41, 48, 49] 147 rigid atoms, others: [1, 3, 4, 5, 6, 26, 27, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 209 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052106 none CC(O)C1CC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 39, 39, 39, 22, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 147, 49, 49, 49, 49, 39, 22, 22, 11, 11, 11, 11, 5, 1] 147 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: 315 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052106 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052106 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052106/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052106 Building REAL250005052107 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052107' /scratch/stefan/7921156/working/building/REAL250005052107 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052107 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052107/0 /scratch/stefan/7921156/working/building/REAL250005052107 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/233 `/scratch/stefan/7921156/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@]12C[C@H]1[C@H](C)C2)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052107.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052107 none CC(CNC(=O)[C@]12C[C@H]1[C@H](C)C2)NC(=O)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', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 41, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 143, 194, 197, 194, 201, 201, 201, 201, 201, 143, 143, 143, 143, 41, 41, 7, 1, 1, 2, 2, 2, 1, 1, 197, 201] 201 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 36, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38]) total number of confs: 800 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: REAL250005052107 none CC(CNC(=O)[C@]12C[C@H]1[C@H](C)C2)NC(=O)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', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 21, 57, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 57, 57, 108, 201, 201, 201, 201, 201, 201, 201, 7, 1] 201 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 520 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052107 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052107 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052107/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052107 Building REAL250005052108 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052108' /scratch/stefan/7921156/working/building/REAL250005052108 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052108 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052108/0 /scratch/stefan/7921156/working/building/REAL250005052108 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/234 `/scratch/stefan/7921156/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN1C=NC=N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052108.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052108 none CC(CNC(=O)CN1C=NC=N1)NC(=O)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.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 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, 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: [180, 133, 41, 41, 8, 41, 1, 1, 1, 1, 1, 1, 180, 201, 201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 180, 133, 133, 41, 8, 8, 1, 1, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 30, 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, 32, 33]) total number of confs: 810 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052108 none CC(CNC(=O)CN1C=NC=N1)NC(=O)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.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 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, 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: [10, 4, 10, 25, 74, 74, 74, 165, 201, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 25, 25, 74, 165, 165, 201, 201, 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: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052108 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052108 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052108/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052108 Building REAL250005052109 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052109' /scratch/stefan/7921156/working/building/REAL250005052109 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052109 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052109/0 /scratch/stefan/7921156/working/building/REAL250005052109 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/235 `/scratch/stefan/7921156/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C#CC1(C)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052109.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052109 none CC(CNC(=O)C#CC1(C)CC1)NC(=O)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 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [36, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 67, 67, 67, 73, 73, 73, 73, 73, 37, 37, 37, 37, 7, 7, 1, 2, 2, 2, 1, 1, 1, 1, 67, 73] 73 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 27, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 35, 36]) total number of confs: 261 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: REAL250005052109 none CC(CNC(=O)C#CC1(C)CC1)NC(=O)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 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [17, 9, 17, 45, 73, 73, 73, 73, 73, 73, 73, 73, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 45, 45, 73, 73, 73, 73, 73, 73, 73, 73, 9, 1] 73 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: 277 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052109 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052109 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052109/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052109 Building REAL250005052110 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052110' /scratch/stefan/7921156/working/building/REAL250005052110 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052110 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052110/0 /scratch/stefan/7921156/working/building/REAL250005052110 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/236 `/scratch/stefan/7921156/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052110.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052110 none CC(CNC(=O)C1=CCC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 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, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [53, 26, 11, 11, 1, 11, 1, 1, 1, 1, 53, 72, 72, 72, 74, 74, 74, 74, 74, 53, 53, 53, 53, 26, 26, 11, 1, 1, 1, 1, 1, 72, 74] 74 rigid atoms, others: [4, 6, 7, 8, 9, 26, 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, 31, 32]) total number of confs: 284 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: REAL250005052110 none CC(CNC(=O)C1=CCC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 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, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 21, 52, 74, 74, 74, 74, 74, 74, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 52, 52, 74, 74, 74, 74, 74, 74, 8, 1] 74 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: 273 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052110 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052110 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052110/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052110 Building REAL250005052111 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052111' /scratch/stefan/7921156/working/building/REAL250005052111 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052111 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052111/0 /scratch/stefan/7921156/working/building/REAL250005052111 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/237 `/scratch/stefan/7921156/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=C(F)O1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052111.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052111 none CC(CNC(=O)C1=CC=C(F)O1)NC(=O)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', 'F', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [92, 44, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 92, 115, 115, 115, 120, 120, 120, 120, 120, 92, 92, 92, 92, 44, 44, 11, 1, 1, 115, 120] 120 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 455 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: REAL250005052111 none CC(CNC(=O)C1=CC=C(F)O1)NC(=O)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', 'F', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 18, 49, 92, 92, 92, 120, 120, 120, 120, 120, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 49, 49, 92, 120, 120, 8, 1] 120 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 378 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052111 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052111 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052111/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052111 Building REAL250005052112 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052112' /scratch/stefan/7921156/working/building/REAL250005052112 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052112 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052112/0 /scratch/stefan/7921156/working/building/REAL250005052112 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/238 `/scratch/stefan/7921156/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052112.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052112 none CON=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 119, 119, 119, 68, 22, 9, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 119, 68, 68, 22, 22, 22, 22, 9, 1] 140 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: 498 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052112 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052112 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052112/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052112 Building REAL250005052113 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052113' /scratch/stefan/7921156/working/building/REAL250005052113 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052113 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052113/0 /scratch/stefan/7921156/working/building/REAL250005052113 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/239 `/scratch/stefan/7921156/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052113.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052113 none C#CCC(C)(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 87, 163, 163, 87, 87, 38, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 163, 163, 163, 163, 163, 163, 87, 38, 38, 13, 13, 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: 853 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052113 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052113 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052113/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052113 Building REAL250005052114 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052114' /scratch/stefan/7921156/working/building/REAL250005052114 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052114 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052114/0 /scratch/stefan/7921156/working/building/REAL250005052114 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/240 `/scratch/stefan/7921156/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN(C)C(N)=O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052114.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052114 none CC(CNC(=O)CN(C)C(N)=O)NC(=O)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.am', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 8, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 10, 26, 65, 65, 65, 164, 192, 192, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 26, 26, 65, 164, 164, 192, 192, 192, 201, 201, 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: 761 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052114 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052114 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052114/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052114 Building REAL250005052115 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052115' /scratch/stefan/7921156/working/building/REAL250005052115 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052115 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052115/0 /scratch/stefan/7921156/working/building/REAL250005052115 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/241 `/scratch/stefan/7921156/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=NC(=O)N[N-]1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052115.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052115 none CC(CNC(=O)C1=NC(=O)N[N-]1)NC(=O)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', 'O.2', 'N.am', 'N.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 1, 11, 8, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [75, 51, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 75, 84, 84, 84, 84, 84, 84, 84, 84, 75, 75, 75, 75, 51, 51, 13, 1, 84, 84] 84 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]) total number of confs: 352 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: REAL250005052115 none CC(CNC(=O)C1=NC(=O)N[N-]1)NC(=O)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', 'O.2', 'N.am', 'N.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 1, 11, 8, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 12, 27, 47, 47, 47, 84, 84, 84, 84, 84, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 27, 47, 84, 4, 1] 84 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 226 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052115 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052115 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052115/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052115 Building REAL250005052116 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052116' /scratch/stefan/7921156/working/building/REAL250005052116 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052116 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052116/0 /scratch/stefan/7921156/working/building/REAL250005052116 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/242 `/scratch/stefan/7921156/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(F)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052116.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052116 none CC(CNC(=O)C1(F)CC1)NC(=O)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.2', 'O.2', 'C.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, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [127, 70, 13, 13, 1, 13, 1, 1, 1, 1, 127, 153, 153, 153, 161, 161, 161, 161, 161, 127, 127, 127, 127, 70, 70, 13, 1, 1, 1, 1, 153, 161] 161 rigid atoms, others: [4, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 628 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: REAL250005052116 none CC(CNC(=O)C1(F)CC1)NC(=O)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.2', 'O.2', 'C.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, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [20, 9, 20, 52, 108, 108, 108, 161, 161, 161, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 52, 52, 108, 161, 161, 161, 161, 9, 1] 161 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: 553 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052116 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052116 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052116/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052116 Building REAL250005052117 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052117' /scratch/stefan/7921156/working/building/REAL250005052117 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052117 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052117/0 /scratch/stefan/7921156/working/building/REAL250005052117 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/243 `/scratch/stefan/7921156/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)COCCO)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052117.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052117 none CC(CNC(=O)COCCO)NC(=O)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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 15, 40, 40, 40, 102, 159, 193, 201, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 15, 40, 102, 102, 193, 193, 201, 201, 603, 2, 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: 1348 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052117 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052117 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052117/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052117 Building REAL250005052118 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052118' /scratch/stefan/7921156/working/building/REAL250005052118 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052118 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052118/0 /scratch/stefan/7921156/working/building/REAL250005052118 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/244 `/scratch/stefan/7921156/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)(C)CF)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052118.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052118 none CC(CNC(=O)C(C)(C)CF)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.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, 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: [14, 5, 14, 44, 103, 103, 103, 187, 187, 187, 201, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 44, 44, 103, 187, 187, 187, 187, 187, 187, 201, 201, 5, 1] 201 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 816 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052118 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052118 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052118/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052118 Building REAL250005052119 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052119' /scratch/stefan/7921156/working/building/REAL250005052119 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052119 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052119/0 /scratch/stefan/7921156/working/building/REAL250005052119 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/245 `/scratch/stefan/7921156/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052119.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052119 none CC(C)[C@@H](O)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 168, 201, 136, 169, 169, 73, 73, 73, 33, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 507, 136, 136, 73, 33, 33, 12, 12, 12, 12, 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: 1437 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052119 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052119 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052119/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052119 Building REAL250005052120 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052120' /scratch/stefan/7921156/working/building/REAL250005052120 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052120 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052120/0 /scratch/stefan/7921156/working/building/REAL250005052120 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/246 `/scratch/stefan/7921156/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005052120.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052120 none CSC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 10, 10, 10, 53, 127, 129, 171, 171, 171, 185, 185, 185, 185, 185, 1, 1, 8, 8, 8, 10, 53, 53, 129, 129, 129, 129, 171, 185, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 35, 33, 34, 18, 19] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 737 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: REAL250005052120 none CSC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 120, 120, 120, 54, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 185, 185, 201, 201, 201, 120, 54, 54, 18, 18, 18, 18, 8, 1, 185, 185, 185, 185] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 634 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052120 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052120 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052120/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052120 Building REAL250005052121 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052121' /scratch/stefan/7921156/working/building/REAL250005052121 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052121 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052121/0 /scratch/stefan/7921156/working/building/REAL250005052121 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/247 `/scratch/stefan/7921156/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=NOCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052121.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052121 none CC(CNC(=O)C1=NOCC1)NC(=O)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.2', 'O.2', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 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: [97, 57, 13, 13, 1, 13, 1, 1, 1, 1, 1, 97, 108, 108, 108, 112, 112, 112, 112, 112, 97, 97, 97, 97, 57, 57, 13, 1, 1, 1, 1, 108, 112] 112 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27, 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, 31, 32]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052121 none CC(CNC(=O)C1=NOCC1)NC(=O)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.2', 'O.2', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 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: [19, 9, 19, 41, 86, 86, 86, 112, 112, 112, 112, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 41, 41, 86, 112, 112, 112, 112, 9, 1] 112 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: 342 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052121 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052121 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052121/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052121 Building REAL250005052122 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052122' /scratch/stefan/7921156/working/building/REAL250005052122 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052122 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052122/0 /scratch/stefan/7921156/working/building/REAL250005052122 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/248 `/scratch/stefan/7921156/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(CCO)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052122.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052122 none CC(CNC(=O)C1(CCO)CC1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [72, 32, 7, 7, 1, 7, 1, 1, 7, 13, 1, 1, 72, 130, 130, 130, 158, 158, 158, 158, 158, 72, 72, 72, 72, 32, 32, 7, 7, 7, 13, 13, 39, 1, 1, 1, 1, 130, 158] 603 rigid atoms, others: [33, 34, 35, 4, 6, 7, 10, 11, 36] set([0, 1, 2, 3, 5, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 625 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052122 none CC(CNC(=O)C1(CCO)CC1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 15, 41, 99, 99, 99, 158, 201, 201, 158, 158, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 41, 41, 99, 201, 201, 201, 201, 603, 158, 158, 158, 158, 5, 1] 603 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 1378 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052122 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052122 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052122/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052122 Building REAL250005052123 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052123' /scratch/stefan/7921156/working/building/REAL250005052123 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052123 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052123/0 /scratch/stefan/7921156/working/building/REAL250005052123 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/249 `/scratch/stefan/7921156/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052123.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052123 none CC(C)C(C)(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 191, 201, 139, 191, 191, 139, 139, 64, 21, 7, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 191, 191, 191, 573, 139, 64, 64, 21, 21, 21, 21, 7, 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: 1349 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052123 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052123 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052123/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052123 Building REAL250005052124 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052124' /scratch/stefan/7921156/working/building/REAL250005052124 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052124 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052124/0 /scratch/stefan/7921156/working/building/REAL250005052124 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/250 `/scratch/stefan/7921156/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)C[NH+](C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052124.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052124 none CC(CNC(=O)C(C)C[NH+](C)C)NC(=O)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.4', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 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, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 9, 15, 15, 15, 16, 16, 16, 16, 16, 16, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 9, 9, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 1] 16 rigid atoms, others: [42, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052124 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052124 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052124/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052124 Building REAL250005052125 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052125' /scratch/stefan/7921156/working/building/REAL250005052125 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052125 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052125/0 /scratch/stefan/7921156/working/building/REAL250005052125 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/251 `/scratch/stefan/7921156/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=NN=CS1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052125.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052125 none CC(CNC(=O)C1=NN=CS1)NC(=O)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.2', 'C.2', 'S.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 14, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 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] 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: [65, 40, 11, 11, 1, 11, 1, 1, 1, 1, 1, 65, 90, 90, 90, 92, 92, 92, 92, 92, 65, 65, 65, 65, 40, 40, 11, 1, 90, 92] 92 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 349 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: REAL250005052125 none CC(CNC(=O)C1=NN=CS1)NC(=O)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.2', 'C.2', 'S.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 14, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 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] 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: [15, 8, 15, 32, 77, 77, 77, 92, 92, 92, 92, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 32, 32, 77, 92, 8, 1] 92 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 285 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052125 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052125 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052125/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052125 Building REAL250005052126 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052126' /scratch/stefan/7921156/working/building/REAL250005052126 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052126 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052126/0 /scratch/stefan/7921156/working/building/REAL250005052126 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/252 `/scratch/stefan/7921156/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(F)C1CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052126.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052126 none CC(CNC(=O)C(F)C1CCC1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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: [181, 125, 39, 39, 7, 39, 1, 7, 1, 1, 1, 1, 181, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 181, 125, 125, 39, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37]) total number of confs: 810 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: REAL250005052126 none CC(CNC(=O)C(F)C1CCC1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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: [11, 4, 11, 30, 88, 88, 88, 166, 166, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 30, 30, 88, 166, 201, 201, 201, 201, 201, 201, 201, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 787 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052126 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052126 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052126/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052126 Building REAL250005052127 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052127' /scratch/stefan/7921156/working/building/REAL250005052127 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052127 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052127/0 /scratch/stefan/7921156/working/building/REAL250005052127 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/253 `/scratch/stefan/7921156/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC(C)(C)O1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052127.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052127 none CC(CNC(=O)C1CC(C)(C)O1)NC(=O)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', '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, 8, 1, 11, 5, 5, 5, 5, 5, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [129, 61, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 129, 153, 154, 153, 158, 158, 158, 158, 158, 129, 129, 129, 129, 61, 61, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 154, 158] 158 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 659 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: REAL250005052127 none CC(CNC(=O)C1CC(C)(C)O1)NC(=O)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', '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, 8, 1, 11, 5, 5, 5, 5, 5, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 18, 45, 102, 102, 102, 158, 158, 158, 158, 158, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 45, 45, 102, 158, 158, 158, 158, 158, 158, 158, 158, 158, 8, 1] 158 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: 529 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052127 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052127 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052127/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052127 Building REAL250005052128 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052128' /scratch/stefan/7921156/working/building/REAL250005052128 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052128 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052128/0 /scratch/stefan/7921156/working/building/REAL250005052128 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/254 `/scratch/stefan/7921156/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=NOC(C)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052128.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052128 none CC(CNC(=O)C1=NOC(C)C1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 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, 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] 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: [105, 61, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 105, 119, 119, 119, 124, 124, 124, 124, 124, 105, 105, 105, 105, 61, 61, 12, 1, 2, 2, 2, 1, 1, 119, 124] 124 rigid atoms, others: [32, 33, 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, 34, 35]) total number of confs: 514 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: REAL250005052128 none CC(CNC(=O)C1=NOC(C)C1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 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, 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] 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: [18, 10, 18, 42, 99, 99, 99, 124, 124, 124, 124, 124, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 42, 42, 99, 124, 124, 124, 124, 124, 124, 10, 1] 124 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: 372 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052128 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052128 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052128/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052128 Building REAL250005052129 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052129' /scratch/stefan/7921156/working/building/REAL250005052129 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052129 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052129/0 /scratch/stefan/7921156/working/building/REAL250005052129 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/255 `/scratch/stefan/7921156/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC(C)(F)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052129.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052129 none CC(CNC(=O)C1CC(C)(F)C1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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: [142, 60, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 142, 189, 189, 189, 201, 201, 201, 201, 201, 142, 142, 142, 142, 60, 60, 12, 1, 1, 1, 2, 2, 2, 1, 1, 189, 201] 201 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 36, 37]) total number of confs: 769 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: REAL250005052129 none CC(CNC(=O)C1CC(C)(F)C1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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: [21, 9, 21, 62, 125, 125, 125, 201, 201, 201, 201, 201, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 62, 62, 125, 201, 201, 201, 201, 201, 201, 201, 201, 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: 657 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052129 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052129 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052129/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052129 Building REAL250005052130 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052130' /scratch/stefan/7921156/working/building/REAL250005052130 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052130 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052130/0 /scratch/stefan/7921156/working/building/REAL250005052130 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/256 `/scratch/stefan/7921156/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052130.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052130 none COCC(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 573 conformations in input total number of sets (complete confs): 573 using faster count positions algorithm for large data unique positions, atoms: [191, 190, 146, 102, 146, 102, 102, 44, 18, 7, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 191, 191, 191, 190, 190, 146, 438, 102, 44, 44, 18, 18, 18, 18, 7, 1] 573 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: 1231 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052130 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052130 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052130/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052130 Building REAL250005052131 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052131' /scratch/stefan/7921156/working/building/REAL250005052131 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052131 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052131/0 /scratch/stefan/7921156/working/building/REAL250005052131 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/257 `/scratch/stefan/7921156/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC(C)(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052131.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052131 none C#CC(C)(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 99, 154, 154, 99, 99, 57, 22, 9, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 154, 154, 154, 99, 57, 57, 22, 22, 22, 22, 9, 1] 154 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: 632 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052131 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052131 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052131/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052131 Building REAL250005052132 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052132' /scratch/stefan/7921156/working/building/REAL250005052132 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052132 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052132/0 /scratch/stefan/7921156/working/building/REAL250005052132 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/258 `/scratch/stefan/7921156/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H]1CNC(=O)N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052132.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052132 none CC(CNC(=O)[C@H]1CNC(=O)N1)NC(=O)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.am', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [115, 61, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 115, 136, 136, 136, 141, 141, 141, 141, 141, 115, 115, 115, 115, 61, 61, 12, 1, 1, 1, 1, 136, 141] 141 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 560 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: REAL250005052132 none CC(CNC(=O)[C@H]1CNC(=O)N1)NC(=O)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.am', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 17, 43, 96, 96, 96, 141, 141, 141, 141, 141, 141, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 43, 43, 96, 141, 141, 141, 141, 8, 1] 141 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 469 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052132 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052132 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052132/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052132 Building REAL250005052133 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052133' /scratch/stefan/7921156/working/building/REAL250005052133 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005052133 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052133/0 /scratch/stefan/7921156/working/building/REAL250005052133 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/259 `/scratch/stefan/7921156/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN1CCC1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052133.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052133 none CC(CNC(=O)CN1CCC1C)NC(=O)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: [176, 108, 30, 30, 5, 30, 1, 1, 1, 1, 1, 1, 176, 195, 195, 195, 201, 201, 201, 201, 201, 176, 176, 176, 176, 108, 108, 30, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 195, 201] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 30, 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, 35, 36, 37, 38, 39]) total number of confs: 807 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: REAL250005052133 none CC(CNC(=O)CN1CCC1C)NC(=O)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: [21, 9, 21, 54, 122, 122, 122, 198, 201, 201, 201, 201, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 54, 54, 122, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 9, 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: 766 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052133 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052133/1 /scratch/stefan/7921156/working/building/REAL250005052133 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/260 `/scratch/stefan/7921156/working/3D/260' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C[N@@H+]1CCC1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052133.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052133/1/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: REAL250005052133 none CC(CNC(=O)C[N@@H+]1CCC1C)NC(=O)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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [24, 21, 16, 16, 5, 16, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 30, 30, 30, 30, 30, 24, 24, 24, 24, 21, 21, 16, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 24, 30] 30 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052133 none CC(CNC(=O)C[N@@H+]1CCC1C)NC(=O)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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 16, 26, 26, 26, 30, 30, 30, 30, 30, 30, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 16, 16, 26, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 1] 30 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: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052133 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `2' /scratch/stefan/7921156/working/building/REAL250005052133/2 /scratch/stefan/7921156/working/building/REAL250005052133 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 2 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/261 `/scratch/stefan/7921156/working/3D/261' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C[N@H+]1CCC1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052133.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005052133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052133/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052133 none CC(CNC(=O)C[N@H+]1CCC1C)NC(=O)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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 13, 13, 6, 13, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 18, 18, 18, 18, 18, 16, 16, 16, 16, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 16, 18] 18 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052133 none CC(CNC(=O)C[N@H+]1CCC1C)NC(=O)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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 12, 15, 15, 15, 18, 18, 18, 18, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 12, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1] 18 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: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052133 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052133 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052133/0.* 2: /scratch/stefan/7921156/working/building/REAL250005052133/2.* 1: /scratch/stefan/7921156/working/building/REAL250005052133/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052133 Building REAL250005052134 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052134' /scratch/stefan/7921156/working/building/REAL250005052134 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052134 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052134/0 /scratch/stefan/7921156/working/building/REAL250005052134 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/262 `/scratch/stefan/7921156/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)COC1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052134.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052134 none CC(CNC(=O)COC1CC1)NC(=O)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, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 160, 87, 87, 22, 87, 6, 1, 1, 1, 1, 188, 201, 201, 201, 201, 201, 201, 201, 201, 188, 188, 188, 188, 160, 160, 87, 22, 22, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 770 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052134 none CC(CNC(=O)COC1CC1)NC(=O)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, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 20, 53, 53, 53, 152, 188, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 53, 152, 152, 201, 201, 201, 201, 201, 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: 689 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052134 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052134 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052134/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052134 Building REAL250005052135 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052135' /scratch/stefan/7921156/working/building/REAL250005052135 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052135 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052135/0 /scratch/stefan/7921156/working/building/REAL250005052135 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/263 `/scratch/stefan/7921156/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=NC=CN1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052135.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052135 none CC(CNC(=O)C1=NC=CN1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 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: [30, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 30, 37, 37, 37, 37, 37, 37, 37, 37, 30, 30, 30, 30, 18, 18, 8, 1, 1, 1, 37, 37] 37 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) 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: REAL250005052135 none CC(CNC(=O)C1=NC=CN1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 31, 42, 42, 42, 45, 45, 45, 45, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 31, 31, 42, 45, 45, 45, 10, 1] 45 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 154 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052135 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052135 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052135/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052135 Building REAL250005052136 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052136' /scratch/stefan/7921156/working/building/REAL250005052136 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052136 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052136/0 /scratch/stefan/7921156/working/building/REAL250005052136 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/264 `/scratch/stefan/7921156/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CC1CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052136.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052136 none CC(CNC(=O)C=CC1CCC1)NC(=O)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: [177, 117, 40, 40, 9, 40, 9, 1, 1, 1, 1, 1, 177, 194, 194, 194, 201, 201, 201, 201, 201, 177, 177, 177, 177, 117, 117, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 194, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38]) total number of confs: 813 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: REAL250005052136 none CC(CNC(=O)C=CC1CCC1)NC(=O)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: [17, 7, 17, 44, 98, 98, 98, 175, 175, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 44, 44, 98, 175, 175, 201, 201, 201, 201, 201, 201, 201, 7, 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: 684 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052136 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052136 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052136/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052136 Building REAL250005052137 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052137' /scratch/stefan/7921156/working/building/REAL250005052137 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052137 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052137/0 /scratch/stefan/7921156/working/building/REAL250005052137 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/265 `/scratch/stefan/7921156/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052137.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052137 none CCCC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 131, 131, 56, 56, 56, 24, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 181, 181, 131, 131, 56, 24, 24, 11, 11, 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: 809 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052137 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052137 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052137/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052137 Building REAL250005052138 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052138' /scratch/stefan/7921156/working/building/REAL250005052138 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052138 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052138/0 /scratch/stefan/7921156/working/building/REAL250005052138 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/266 `/scratch/stefan/7921156/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052138.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052138 none CC=C(F)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 77, 85, 77, 77, 51, 20, 8, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 77, 51, 51, 20, 20, 20, 20, 8, 1] 85 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: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052138 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052138 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052138/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052138 Building REAL250005052139 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052139' /scratch/stefan/7921156/working/building/REAL250005052139 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052139 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052139/0 /scratch/stefan/7921156/working/building/REAL250005052139 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/267 `/scratch/stefan/7921156/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005052139.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052139 none CCC(C(=O)NCC(C)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [177, 171, 101, 101, 101, 47, 18, 11, 18, 11, 1, 11, 1, 1, 1, 1, 1, 1, 171, 195, 192, 188, 188, 188, 188, 188, 171, 101, 47, 47, 18, 18, 18, 18, 11, 1, 195, 195, 195, 195, 195, 195, 195] 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: 998 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052139 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052139 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052139/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052139 Building REAL250005052140 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052140' /scratch/stefan/7921156/working/building/REAL250005052140 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052140 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052140/0 /scratch/stefan/7921156/working/building/REAL250005052140 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/268 `/scratch/stefan/7921156/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(F)=C1CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052140.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052140 none CC(CNC(=O)C(F)=C1CCC1)NC(=O)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', 'F', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 15, 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, 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 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [128, 60, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 128, 162, 162, 162, 169, 169, 169, 169, 169, 128, 128, 128, 128, 60, 60, 11, 1, 1, 1, 1, 1, 1, 162, 169] 169 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 28, 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, 34, 35]) total number of confs: 661 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: REAL250005052140 none CC(CNC(=O)C(F)=C1CCC1)NC(=O)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', 'F', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 15, 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, 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 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 50, 116, 116, 116, 168, 169, 169, 169, 168, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 50, 50, 116, 169, 169, 169, 169, 169, 169, 8, 1] 169 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: 577 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052140 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052140 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052140/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052140 Building REAL250005052141 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052141' /scratch/stefan/7921156/working/building/REAL250005052141 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052141 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052141/0 /scratch/stefan/7921156/working/building/REAL250005052141 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/269 `/scratch/stefan/7921156/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CO)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052141.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052141 none CCC(CO)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [172, 156, 83, 156, 194, 83, 83, 35, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 182, 182, 182, 182, 182, 156, 194, 194, 582, 83, 35, 35, 14, 14, 14, 14, 7, 1] 603 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1601 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052141 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052141 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052141/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052141 Building REAL250005052142 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052142' /scratch/stefan/7921156/working/building/REAL250005052142 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052142 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052142/0 /scratch/stefan/7921156/working/building/REAL250005052142 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/270 `/scratch/stefan/7921156/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)CO)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052142.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052142 none CC(CNC(=O)C(C)CO)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 17, 44, 105, 105, 105, 194, 194, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 44, 44, 105, 194, 194, 194, 194, 201, 201, 603, 7, 1] 603 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1388 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052142 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052142 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052142/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052142 Building REAL250005052143 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052143' /scratch/stefan/7921156/working/building/REAL250005052143 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052143 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052143/0 /scratch/stefan/7921156/working/building/REAL250005052143 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/271 `/scratch/stefan/7921156/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CON=C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052143.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052143 none CC(CNC(=O)C1=CON=C1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 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: [98, 30, 5, 5, 1, 5, 1, 1, 1, 1, 1, 100, 124, 124, 124, 133, 133, 133, 133, 133, 100, 100, 100, 100, 30, 30, 5, 1, 1, 124, 133] 133 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 506 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: REAL250005052143 none CC(CNC(=O)C1=CON=C1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 17, 44, 88, 88, 88, 133, 133, 133, 133, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 44, 44, 88, 133, 133, 8, 1] 133 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 400 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052143 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052143 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052143/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052143 Building REAL250005052144 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052144' /scratch/stefan/7921156/working/building/REAL250005052144 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052144 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052144/0 /scratch/stefan/7921156/working/building/REAL250005052144 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/272 `/scratch/stefan/7921156/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1C[C@H]1CF)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052144.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052144 none CC(CNC(=O)[C@@H]1C[C@H]1CF)NC(=O)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.2', 'O.2', 'C.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, 5, 15, 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, 7, 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: [126, 59, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 9, 126, 189, 189, 189, 192, 192, 192, 192, 192, 126, 126, 126, 126, 59, 59, 13, 1, 1, 9, 9, 189, 192] 201 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]) total number of confs: 778 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: REAL250005052144 none CC(CNC(=O)[C@@H]1C[C@H]1CF)NC(=O)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.2', 'O.2', 'C.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, 5, 15, 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, 7, 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: [10, 4, 10, 27, 74, 74, 74, 192, 192, 192, 192, 192, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 27, 27, 74, 192, 192, 201, 201, 4, 1] 201 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 619 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052144 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052144 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052144/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052144 Building REAL250005052145 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052145' /scratch/stefan/7921156/working/building/REAL250005052145 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052145 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052145/0 /scratch/stefan/7921156/working/building/REAL250005052145 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/273 `/scratch/stefan/7921156/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005052145.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052145 none C#CC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 134, 138, 188, 190, 188, 201, 201, 201, 201, 201, 1, 1, 1, 7, 44, 44, 138, 138, 138, 138, 190, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 32, 18, 19, 20, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 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: REAL250005052145 none C#CC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 58, 21, 8, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 100, 58, 58, 21, 21, 21, 21, 8, 1, 201, 201, 201, 201] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 652 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052145 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052145 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052145/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052145 Building REAL250005052146 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052146' /scratch/stefan/7921156/working/building/REAL250005052146 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052146 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052146/0 /scratch/stefan/7921156/working/building/REAL250005052146 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/274 `/scratch/stefan/7921156/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=COCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052146.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052146 none CC(CNC(=O)C1=COCC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 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, 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 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [97, 48, 11, 11, 1, 11, 1, 1, 1, 1, 1, 97, 125, 125, 125, 127, 127, 127, 127, 127, 97, 97, 97, 97, 48, 48, 11, 1, 1, 1, 1, 1, 125, 127] 127 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27, 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, 32, 33]) total number of confs: 500 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: REAL250005052146 none CC(CNC(=O)C1=COCC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 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, 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 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 19, 52, 95, 95, 95, 127, 127, 127, 127, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 52, 52, 95, 127, 127, 127, 127, 127, 7, 1] 127 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: 399 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052146 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052146 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052146/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052146 Building REAL250005052147 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052147' /scratch/stefan/7921156/working/building/REAL250005052147 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052147 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052147/0 /scratch/stefan/7921156/working/building/REAL250005052147 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/275 `/scratch/stefan/7921156/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H](C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052147.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052147 none 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', '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'] dock atom type numbers: [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, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 357 conformations in input total number of sets (complete confs): 357 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 46, 92, 92, 92, 119, 119, 119, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 46, 46, 92, 119, 119, 119, 357, 8, 1] 357 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: 825 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052147 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052147 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052147/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052147 Building REAL250005052148 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052148' /scratch/stefan/7921156/working/building/REAL250005052148 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052148 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052148/0 /scratch/stefan/7921156/working/building/REAL250005052148 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/276 `/scratch/stefan/7921156/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(F)=NN1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052148.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052148 none CC(CNC(=O)C1=CC(F)=NN1)NC(=O)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', 'F', 'N.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 15, 8, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [73, 38, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 74, 100, 100, 100, 105, 105, 105, 105, 105, 74, 74, 74, 74, 38, 38, 9, 1, 1, 100, 105] 105 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 413 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: REAL250005052148 none CC(CNC(=O)C1=CC(F)=NN1)NC(=O)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', 'F', 'N.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 15, 8, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 49, 86, 86, 86, 105, 105, 105, 105, 105, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 49, 49, 86, 105, 105, 8, 1] 105 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 353 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052148 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052148 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052148/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052148 Building REAL250005052149 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052149' /scratch/stefan/7921156/working/building/REAL250005052149 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052149 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052149/0 /scratch/stefan/7921156/working/building/REAL250005052149 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/277 `/scratch/stefan/7921156/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1C=CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052149.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052149 none CC(CNC(=O)C1C=CCC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 1, 1, 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 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [149, 63, 12, 12, 1, 12, 1, 1, 1, 1, 1, 149, 180, 180, 180, 188, 188, 188, 188, 188, 149, 149, 149, 149, 63, 63, 12, 1, 1, 1, 1, 1, 1, 1, 180, 188] 188 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 27, 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, 34, 35]) total number of confs: 739 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: REAL250005052149 none CC(CNC(=O)C1C=CCC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 1, 1, 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 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [20, 9, 20, 57, 117, 117, 117, 188, 188, 188, 188, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 57, 57, 117, 188, 188, 188, 188, 188, 188, 188, 9, 1] 188 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: 622 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052149 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052149 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052149/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052149 Building REAL250005052150 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052150' /scratch/stefan/7921156/working/building/REAL250005052150 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052150 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052150/0 /scratch/stefan/7921156/working/building/REAL250005052150 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/278 `/scratch/stefan/7921156/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052150.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052150 none CC(O)C(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [163, 152, 165, 99, 152, 99, 99, 44, 18, 10, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 495, 152, 152, 152, 152, 99, 44, 44, 18, 18, 18, 18, 10, 1] 495 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: 1154 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052150 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052150 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052150/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052150 Building REAL250005052151 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052151' /scratch/stefan/7921156/working/building/REAL250005052151 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052151 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052151/0 /scratch/stefan/7921156/working/building/REAL250005052151 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/279 `/scratch/stefan/7921156/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(O)CCOC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052151.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052151 none CC(CNC(=O)C1(O)CCOC1)NC(=O)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', '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, 5, 12, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 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] 1 hydrogens need rotated 459 conformations in input total number of sets (complete confs): 459 using faster count positions algorithm for large data unique positions, atoms: [111, 53, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 111, 143, 143, 143, 153, 153, 153, 153, 153, 111, 111, 111, 111, 53, 53, 11, 6, 1, 1, 1, 1, 1, 1, 143, 153] 459 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]) total number of confs: 597 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: REAL250005052151 none CC(CNC(=O)C1(O)CCOC1)NC(=O)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', '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, 5, 12, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 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] 1 hydrogens need rotated 459 conformations in input total number of sets (complete confs): 459 using faster count positions algorithm for large data unique positions, atoms: [22, 11, 22, 49, 106, 106, 106, 153, 153, 153, 153, 153, 11, 1, 11, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 49, 49, 106, 459, 153, 153, 153, 153, 153, 153, 11, 1] 459 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: 970 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052151 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052151 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052151/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052151 Building REAL250005052152 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052152' /scratch/stefan/7921156/working/building/REAL250005052152 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052152 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052152/0 /scratch/stefan/7921156/working/building/REAL250005052152 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/280 `/scratch/stefan/7921156/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052152.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052152 none C=C1CC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 73, 157, 158, 186, 186, 186, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 13, 73, 73, 158, 158, 158, 158, 186, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 799 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: REAL250005052152 none C=C1CC1C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 123, 123, 60, 23, 10, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 123, 60, 60, 23, 23, 23, 23, 10, 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: 655 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052152 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052152 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052152/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052152 Building REAL250005052153 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052153' /scratch/stefan/7921156/working/building/REAL250005052153 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052153 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052153/0 /scratch/stefan/7921156/working/building/REAL250005052153 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/281 `/scratch/stefan/7921156/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CC=CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052153.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052153 none CC(CNC(=O)CC1CC=CC1)NC(=O)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.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 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: [187, 125, 33, 33, 6, 33, 1, 1, 1, 1, 1, 1, 187, 201, 201, 201, 201, 201, 201, 201, 201, 187, 187, 187, 187, 125, 125, 33, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 30, 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, 37, 38]) total number of confs: 835 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: REAL250005052153 none CC(CNC(=O)CC1CC=CC1)NC(=O)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.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 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: [12, 4, 12, 33, 80, 80, 80, 189, 201, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 33, 33, 80, 189, 189, 201, 201, 201, 201, 201, 201, 201, 4, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 776 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052153 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052153 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052153/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052153 Building REAL250005052154 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052154' /scratch/stefan/7921156/working/building/REAL250005052154 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052154 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052154/0 /scratch/stefan/7921156/working/building/REAL250005052154 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/282 `/scratch/stefan/7921156/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)CF)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052154.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052154 none CC(CNC(=O)C(C)CF)NC(=O)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.2', 'O.2', 'C.2', 'C.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, 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: [15, 6, 15, 42, 96, 96, 96, 194, 194, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 42, 42, 96, 194, 194, 194, 194, 201, 201, 6, 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: 781 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052154 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052154 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052154/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052154 Building REAL250005052155 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052155' /scratch/stefan/7921156/working/building/REAL250005052155 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052155 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052155/0 /scratch/stefan/7921156/working/building/REAL250005052155 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/283 `/scratch/stefan/7921156/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(C)(C)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052155.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052155 none CC(CNC(=O)C1=CC(C)(C)C1)NC(=O)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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [73, 36, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 74, 95, 95, 95, 99, 99, 99, 99, 99, 74, 74, 74, 74, 36, 36, 10, 1, 2, 2, 2, 2, 2, 2, 1, 1, 95, 99] 99 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 36, 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, 37, 38]) total number of confs: 393 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: REAL250005052155 none CC(CNC(=O)C1=CC(C)(C)C1)NC(=O)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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [20, 9, 20, 52, 95, 95, 95, 99, 99, 99, 99, 99, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 52, 52, 95, 99, 99, 99, 99, 99, 99, 99, 99, 99, 9, 1] 99 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: 334 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052155 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052155 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052155/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052155 Building REAL250005052156 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052156' /scratch/stefan/7921156/working/building/REAL250005052156 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052156 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052156/0 /scratch/stefan/7921156/working/building/REAL250005052156 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/284 `/scratch/stefan/7921156/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1CC1(F)F)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052156.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052156 none CC(CNC(=O)[C@@H]1CC1(F)F)NC(=O)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', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 69, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 151, 195, 195, 195, 201, 201, 201, 201, 201, 151, 151, 151, 151, 69, 69, 13, 1, 1, 195, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 788 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: REAL250005052156 none CC(CNC(=O)[C@@H]1CC1(F)F)NC(=O)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', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 7, 22, 61, 119, 119, 119, 201, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 61, 61, 119, 201, 201, 8, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 679 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052156 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052156 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052156/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052156 Building REAL250005052157 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052157' /scratch/stefan/7921156/working/building/REAL250005052157 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052157 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052157/0 /scratch/stefan/7921156/working/building/REAL250005052157 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/285 `/scratch/stefan/7921156/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052157.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052157 none CC(=O)NCCC(=O)NCC(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 174, 161, 77, 77, 77, 37, 15, 8, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 174, 174, 161, 161, 77, 37, 37, 15, 15, 15, 15, 8, 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: 806 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052157 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052157 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052157/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052157 Building REAL250005052158 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052158' /scratch/stefan/7921156/working/building/REAL250005052158 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052158 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052158/0 /scratch/stefan/7921156/working/building/REAL250005052158 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/286 `/scratch/stefan/7921156/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CNC(=O)N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052158.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052158 none CC(CNC(=O)C1=CNC(=O)N1)NC(=O)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.am', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [92, 43, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 93, 123, 123, 123, 128, 128, 128, 128, 128, 93, 93, 93, 93, 43, 43, 9, 1, 1, 1, 123, 128] 128 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32]) total number of confs: 508 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: REAL250005052158 none CC(CNC(=O)C1=CNC(=O)N1)NC(=O)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.am', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 50, 99, 99, 99, 128, 128, 128, 128, 128, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 99, 128, 128, 128, 7, 1] 128 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: 401 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052158 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052158 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052158/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052158 Building REAL250005052159 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052159' /scratch/stefan/7921156/working/building/REAL250005052159 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052159 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052159/0 /scratch/stefan/7921156/working/building/REAL250005052159 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/287 `/scratch/stefan/7921156/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCCC1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052159.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052159 none CC(CNC(=O)C1CCCC1C)NC(=O)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: [146, 56, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 147, 194, 194, 194, 201, 201, 201, 201, 201, 147, 147, 147, 147, 56, 56, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 194, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 28, 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, 36, 37, 38, 39, 40]) total number of confs: 785 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052159 none CC(CNC(=O)C1CCCC1C)NC(=O)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: [20, 8, 20, 62, 131, 131, 131, 201, 201, 201, 201, 201, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 62, 62, 131, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 680 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052159 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052159 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052159/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052159 Building REAL250005052160 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052160' /scratch/stefan/7921156/working/building/REAL250005052160 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052160 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052160/0 /scratch/stefan/7921156/working/building/REAL250005052160 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/288 `/scratch/stefan/7921156/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052160.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052160 none C=C(C)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 201, 121, 121, 121, 60, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 198, 198, 121, 60, 60, 18, 18, 18, 18, 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: 808 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052160 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052160 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052160/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052160 Building REAL250005052161 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052161' /scratch/stefan/7921156/working/building/REAL250005052161 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052161 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052161/0 /scratch/stefan/7921156/working/building/REAL250005052161 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/289 `/scratch/stefan/7921156/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052161.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052161 none CCSCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 169, 127, 76, 76, 76, 27, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 127, 127, 76, 27, 27, 11, 11, 11, 11, 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: 757 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052161 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052161 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052161/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052161 Building REAL250005052162 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052162' /scratch/stefan/7921156/working/building/REAL250005052162 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052162 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052162/0 /scratch/stefan/7921156/working/building/REAL250005052162 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/290 `/scratch/stefan/7921156/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052162.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052162 none CC(C)=C(C)C(=O)NCC(C)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 89, 119, 89, 89, 43, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119, 119, 119, 89, 43, 43, 18, 18, 18, 18, 8, 1] 119 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: 420 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052162 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052162 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052162/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052162 Building REAL250005052163 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052163' /scratch/stefan/7921156/working/building/REAL250005052163 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052163 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052163/0 /scratch/stefan/7921156/working/building/REAL250005052163 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/291 `/scratch/stefan/7921156/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052163.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052163 none CCCC(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 143, 110, 143, 110, 110, 45, 15, 4, 15, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 190, 190, 143, 429, 110, 45, 45, 15, 15, 15, 15, 4, 1] 603 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1280 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052163 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052163 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052163/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052163 Building REAL250005052164 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052164' /scratch/stefan/7921156/working/building/REAL250005052164 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052164 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052164/0 /scratch/stefan/7921156/working/building/REAL250005052164 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/292 `/scratch/stefan/7921156/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052164.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052164 none CCCCC(O)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 173, 100, 72, 100, 72, 72, 28, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 183, 183, 173, 173, 100, 300, 72, 28, 28, 11, 11, 11, 11, 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: 1218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052164 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052164 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052164/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052164 Building REAL250005052165 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052165' /scratch/stefan/7921156/working/building/REAL250005052165 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052165 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052165/0 /scratch/stefan/7921156/working/building/REAL250005052165 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/293 `/scratch/stefan/7921156/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CSC1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052165.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052165 none CC(CNC(=O)CSC1CC1)NC(=O)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', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 14, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 158, 75, 75, 32, 75, 6, 1, 1, 1, 1, 186, 201, 201, 201, 201, 201, 201, 201, 201, 186, 186, 186, 186, 158, 158, 75, 32, 32, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) 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: REAL250005052165 none CC(CNC(=O)CSC1CC1)NC(=O)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', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 14, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 20, 46, 46, 46, 119, 166, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 46, 119, 119, 201, 201, 201, 201, 201, 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: 677 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052165 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052165 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052165/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052165 Building REAL250005052166 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052166' /scratch/stefan/7921156/working/building/REAL250005052166 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052166 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052166/0 /scratch/stefan/7921156/working/building/REAL250005052166 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/294 `/scratch/stefan/7921156/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052166.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052166 none CCC(O)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 504 conformations in input total number of sets (complete confs): 504 using faster count positions algorithm for large data unique positions, atoms: [168, 158, 119, 159, 68, 68, 68, 29, 13, 5, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 168, 159, 477, 119, 119, 68, 29, 29, 13, 13, 13, 13, 5, 1] 504 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: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052166 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052166 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052166/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052166 Building REAL250005052167 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052167' /scratch/stefan/7921156/working/building/REAL250005052167 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052167 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052167/0 /scratch/stefan/7921156/working/building/REAL250005052167 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/295 `/scratch/stefan/7921156/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(Cl)=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052167.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052167 none CC(Cl)=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 104, 104, 104, 55, 20, 10, 20, 10, 1, 10, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 104, 55, 55, 20, 20, 20, 20, 10, 1] 128 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 447 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052167 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052167 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052167/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052167 Building REAL250005052168 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052168' /scratch/stefan/7921156/working/building/REAL250005052168 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052168 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052168/0 /scratch/stefan/7921156/working/building/REAL250005052168 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/296 `/scratch/stefan/7921156/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052168.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052168 none CC=CC(=O)NCC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 76, 76, 76, 49, 20, 8, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 76, 49, 49, 20, 20, 20, 20, 8, 1] 95 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: 349 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052168 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052168 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052168/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052168 Building REAL250005052169 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052169' /scratch/stefan/7921156/working/building/REAL250005052169 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052169 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052169/0 /scratch/stefan/7921156/working/building/REAL250005052169 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/297 `/scratch/stefan/7921156/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)(F)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052169.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052169 none CCC(F)(F)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 189, 93, 189, 189, 93, 93, 38, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 93, 38, 38, 13, 13, 13, 13, 4, 1] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 936 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052169 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052169 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052169/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052169 Building REAL250005052170 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052170' /scratch/stefan/7921156/working/building/REAL250005052170 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052170 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052170/0 /scratch/stefan/7921156/working/building/REAL250005052170 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/298 `/scratch/stefan/7921156/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(C)CC1F)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052170.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052170 none CC(CNC(=O)C1(C)CC1F)NC(=O)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.2', 'O.2', 'C.2', 'C.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, 5, 15, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [124, 41, 6, 6, 1, 6, 1, 1, 1, 1, 1, 125, 174, 176, 174, 182, 182, 182, 182, 182, 125, 125, 125, 125, 41, 41, 6, 2, 2, 2, 1, 1, 1, 176, 182] 182 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 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, 29, 33, 34]) total number of confs: 723 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: REAL250005052170 none CC(CNC(=O)C1(C)CC1F)NC(=O)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.2', 'O.2', 'C.2', 'C.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, 5, 15, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [24, 8, 24, 65, 125, 125, 125, 182, 182, 182, 182, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 65, 65, 125, 182, 182, 182, 182, 182, 182, 8, 1] 182 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: 626 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052170 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052170 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052170/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052170 Building REAL250005052171 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052171' /scratch/stefan/7921156/working/building/REAL250005052171 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052171 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052171/0 /scratch/stefan/7921156/working/building/REAL250005052171 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/299 `/scratch/stefan/7921156/working/3D/299' -> `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)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052171.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052171 none CC(CNC(=O)[C@H]1C[C@@H](O)C1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 7, 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, 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] 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: [143, 61, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 144, 190, 191, 190, 201, 201, 201, 201, 201, 144, 144, 144, 144, 61, 61, 13, 1, 1, 6, 1, 1, 191, 201] 603 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 29, 30] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 34, 35]) total number of confs: 774 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: REAL250005052171 none CC(CNC(=O)[C@H]1C[C@@H](O)C1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 7, 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, 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] 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: [20, 7, 20, 58, 129, 129, 129, 201, 201, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 58, 58, 129, 201, 201, 603, 201, 201, 8, 1] 603 rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1278 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052171 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052171 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052171/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052171 Building REAL250005052172 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052172' /scratch/stefan/7921156/working/building/REAL250005052172 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052172 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052172/0 /scratch/stefan/7921156/working/building/REAL250005052172 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/300 `/scratch/stefan/7921156/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CC1(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052172.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052172 none CC(CNC(=O)CC1CC1(C)C)NC(=O)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: [183, 124, 36, 36, 5, 36, 1, 1, 1, 1, 1, 1, 183, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 183, 183, 124, 124, 36, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 201, 201] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 30, 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, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 848 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: REAL250005052172 none CC(CNC(=O)CC1CC1(C)C)NC(=O)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: [10, 4, 10, 29, 76, 76, 76, 191, 201, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 29, 29, 76, 191, 191, 201, 201, 201, 201, 201, 201, 201, 201, 201, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 787 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052172 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052172 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052172/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052172 Building REAL250005052173 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052173' /scratch/stefan/7921156/working/building/REAL250005052173 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052173 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052173/0 /scratch/stefan/7921156/working/building/REAL250005052173 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/301 `/scratch/stefan/7921156/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)NC(N)=O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052173.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052173 none CC(CNC(=O)C(C)NC(N)=O)NC(=O)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.am', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 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] 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: [18, 10, 18, 41, 91, 91, 91, 163, 163, 163, 163, 163, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 41, 41, 91, 163, 163, 163, 163, 163, 163, 163, 10, 1] 163 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: 638 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052173 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052173 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052173/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052173 Building REAL250005052174 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052174' /scratch/stefan/7921156/working/building/REAL250005052174 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052174 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052174/0 /scratch/stefan/7921156/working/building/REAL250005052174 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/302 `/scratch/stefan/7921156/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052174.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052174 none C=C(C)CCCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 119, 41, 41, 41, 18, 8, 4, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 187, 188, 154, 154, 119, 119, 41, 18, 18, 8, 8, 8, 8, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1007 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052174 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052174 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052174/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052174 Building REAL250005052175 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052175' /scratch/stefan/7921156/working/building/REAL250005052175 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052175 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052175/0 /scratch/stefan/7921156/working/building/REAL250005052175 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/303 `/scratch/stefan/7921156/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(C)CC(F)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052175.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052175 none CC(CNC(=O)C1(C)CC(F)C1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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: [121, 37, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 123, 192, 193, 192, 201, 201, 201, 201, 201, 123, 123, 123, 123, 37, 37, 6, 2, 2, 2, 1, 1, 1, 1, 1, 193, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 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, 30, 36, 37]) total number of confs: 766 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: REAL250005052175 none CC(CNC(=O)C1(C)CC(F)C1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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: [20, 7, 20, 62, 118, 118, 118, 201, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 62, 62, 118, 201, 201, 201, 201, 201, 201, 201, 201, 7, 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: 676 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052175 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052175 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052175/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052175 Building REAL250005052176 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052176' /scratch/stefan/7921156/working/building/REAL250005052176 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052176 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052176/0 /scratch/stefan/7921156/working/building/REAL250005052176 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/304 `/scratch/stefan/7921156/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052176.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052176 none CC(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', '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'] dock atom type numbers: [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, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 67, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 149, 193, 193, 193, 201, 201, 201, 201, 201, 149, 149, 149, 149, 67, 67, 13, 1, 1, 2, 2, 2, 193, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 796 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: REAL250005052176 none CC(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', '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'] dock atom type numbers: [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, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 7, 22, 64, 127, 127, 127, 201, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 64, 64, 127, 201, 201, 201, 201, 201, 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: 687 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052176 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052176 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052176/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052176 Building REAL250005052177 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052177' /scratch/stefan/7921156/working/building/REAL250005052177 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052177 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052177/0 /scratch/stefan/7921156/working/building/REAL250005052177 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/305 `/scratch/stefan/7921156/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1CC[C@@H]2C[C@@H]21)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052177.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052177 none CC(CNC(=O)[C@@H]1CC[C@@H]2C[C@@H]21)NC(=O)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', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 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, 7, 7, 7, 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: [160, 73, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 161, 195, 195, 195, 201, 201, 201, 201, 201, 161, 161, 161, 161, 73, 73, 13, 1, 1, 1, 1, 1, 1, 195, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36, 31] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38]) total number of confs: 805 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: REAL250005052177 none CC(CNC(=O)[C@@H]1CC[C@@H]2C[C@@H]21)NC(=O)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', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 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, 7, 7, 7, 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, 7, 19, 61, 120, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 61, 61, 120, 201, 201, 201, 201, 201, 201, 7, 1] 201 rigid atoms, others: [38, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 673 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052177 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052177 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052177/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052177 Building REAL250005052178 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052178' /scratch/stefan/7921156/working/building/REAL250005052178 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052178 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052178/0 /scratch/stefan/7921156/working/building/REAL250005052178 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/306 `/scratch/stefan/7921156/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)COC1COC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052178.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052178 none CC(CNC(=O)COC1COC1)NC(=O)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', '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, 5, 12, 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, 3, 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: [192, 160, 73, 73, 22, 73, 6, 1, 1, 1, 1, 1, 192, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 192, 192, 160, 160, 73, 22, 22, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 814 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052178 none CC(CNC(=O)COC1COC1)NC(=O)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', '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, 5, 12, 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, 3, 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: [7, 4, 7, 17, 38, 38, 38, 124, 171, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 17, 17, 38, 124, 124, 201, 201, 201, 201, 201, 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: 648 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052178 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052178 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052178/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052178 Building REAL250005052179 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052179' /scratch/stefan/7921156/working/building/REAL250005052179 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052179 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052179/0 /scratch/stefan/7921156/working/building/REAL250005052179 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/307 `/scratch/stefan/7921156/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@]12C[C@@H]1[C@H](C)C2)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052179.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052179 none CC(CNC(=O)[C@@]12C[C@@H]1[C@H](C)C2)NC(=O)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', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 42, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 137, 192, 192, 192, 201, 201, 201, 201, 201, 137, 137, 137, 137, 42, 42, 7, 1, 1, 2, 2, 2, 1, 1, 192, 201] 201 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 36, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38]) total number of confs: 783 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: REAL250005052179 none CC(CNC(=O)[C@@]12C[C@@H]1[C@H](C)C2)NC(=O)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', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 20, 60, 94, 94, 94, 201, 201, 201, 201, 201, 201, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 60, 60, 94, 201, 201, 201, 201, 201, 201, 201, 6, 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: 500 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052179 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052179 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052179/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052179 Building REAL250005052180 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052180' /scratch/stefan/7921156/working/building/REAL250005052180 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052180 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052180/0 /scratch/stefan/7921156/working/building/REAL250005052180 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/308 `/scratch/stefan/7921156/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052180.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052180 none CNC(=O)CC(=O)NCC(C)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 40, 47, 31, 31, 31, 13, 8, 3, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 40, 40, 31, 13, 13, 8, 8, 8, 8, 3, 1] 47 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052180 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052180 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052180/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052180 Building REAL250005052181 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052181' /scratch/stefan/7921156/working/building/REAL250005052181 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052181 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052181/0 /scratch/stefan/7921156/working/building/REAL250005052181 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/309 `/scratch/stefan/7921156/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC=CCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052181.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052181 none C=CC=CCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 148, 67, 67, 67, 33, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 148, 148, 67, 33, 33, 13, 13, 13, 13, 4, 1] 201 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 785 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052181 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052181 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052181/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052181 Building REAL250005052182 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052182' /scratch/stefan/7921156/working/building/REAL250005052182 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052182 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052182/0 /scratch/stefan/7921156/working/building/REAL250005052182 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/310 `/scratch/stefan/7921156/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005052182.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052182 none C#CC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 129, 132, 193, 194, 193, 201, 201, 201, 201, 201, 1, 1, 1, 1, 7, 40, 40, 132, 132, 132, 132, 194, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 36, 33, 35, 32, 34, 18, 19, 20, 21, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 767 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: REAL250005052182 none C#CC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 109, 109, 109, 58, 22, 8, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 109, 58, 58, 22, 22, 22, 22, 8, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 666 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052182 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052182 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052182/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052182 Building REAL250005052183 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052183' /scratch/stefan/7921156/working/building/REAL250005052183 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005052183 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052183/0 /scratch/stefan/7921156/working/building/REAL250005052183 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/311 `/scratch/stefan/7921156/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1CCC[N@@H+]1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052183.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052183 none CC(CNC(=O)[C@@H]1CCC[N@@H+]1C)NC(=O)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', 'N.4', '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, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 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, 1, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [8, 6, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 11, 11, 11, 11, 11, 8, 8, 8, 8, 6, 6, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 11] 11 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40]) total number of confs: 42 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: REAL250005052183 none CC(CNC(=O)[C@@H]1CCC[N@@H+]1C)NC(=O)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', 'N.4', '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, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 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, 1, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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, 6, 7, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1] 11 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: 38 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052183 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052183/1 /scratch/stefan/7921156/working/building/REAL250005052183 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/312 `/scratch/stefan/7921156/working/3D/312' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1CCC[N@H+]1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052183.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052183/1/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: REAL250005052183 none CC(CNC(=O)[C@@H]1CCC[N@H+]1C)NC(=O)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', 'N.4', '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, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 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, 1, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 14, 14, 14, 14, 14, 12, 12, 12, 12, 10, 10, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 14] 14 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052183 none CC(CNC(=O)[C@@H]1CCC[N@H+]1C)NC(=O)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', 'N.4', '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, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 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, 1, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [9, 6, 9, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1] 14 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: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052183 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `2' /scratch/stefan/7921156/working/building/REAL250005052183/2 /scratch/stefan/7921156/working/building/REAL250005052183 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 2 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/313 `/scratch/stefan/7921156/working/3D/313' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1CCCN1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052183.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005052183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052183/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052183 none CC(CNC(=O)[C@@H]1CCCN1C)NC(=O)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', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 10, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [101, 50, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 101, 125, 125, 125, 131, 131, 131, 131, 131, 101, 101, 101, 101, 50, 50, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 125, 131] 131 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39]) total number of confs: 527 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: REAL250005052183 none CC(CNC(=O)[C@@H]1CCCN1C)NC(=O)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', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 10, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [19, 8, 19, 46, 89, 89, 89, 131, 131, 131, 131, 131, 131, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 46, 46, 89, 131, 131, 131, 131, 131, 131, 131, 131, 131, 8, 1] 131 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: 450 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052183 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052183 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052183/0.* 2: /scratch/stefan/7921156/working/building/REAL250005052183/2.* 1: /scratch/stefan/7921156/working/building/REAL250005052183/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052183 Building REAL250005052184 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052184' /scratch/stefan/7921156/working/building/REAL250005052184 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052184 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052184/0 /scratch/stefan/7921156/working/building/REAL250005052184 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/314 `/scratch/stefan/7921156/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC=CCO1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052184.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052184 none CC(CNC(=O)C1CC=CCO1)NC(=O)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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [119, 66, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 119, 140, 140, 140, 142, 142, 142, 142, 142, 119, 119, 119, 119, 66, 66, 13, 1, 1, 1, 1, 1, 1, 1, 140, 142] 142 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 28, 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, 35, 36]) total number of confs: 586 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: REAL250005052184 none CC(CNC(=O)C1CC=CCO1)NC(=O)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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 14, 37, 90, 90, 90, 142, 142, 142, 142, 142, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 37, 37, 90, 142, 142, 142, 142, 142, 142, 142, 7, 1] 142 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: 465 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052184 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052184 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052184/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052184 Building REAL250005052185 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052185' /scratch/stefan/7921156/working/building/REAL250005052185 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052185 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052185/0 /scratch/stefan/7921156/working/building/REAL250005052185 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/315 `/scratch/stefan/7921156/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCOC1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052185.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052185 none CC(CNC(=O)CCOC1CC1)NC(=O)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, 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, 7, 7] 0 hydrogens 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, 182, 126, 126, 39, 126, 21, 6, 1, 1, 1, 1, 197, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 197, 197, 182, 182, 126, 39, 39, 21, 21, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) 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: REAL250005052185 none CC(CNC(=O)CCOC1CC1)NC(=O)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, 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, 7, 7] 0 hydrogens 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, 4, 6, 14, 31, 31, 31, 105, 126, 173, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 31, 105, 105, 126, 126, 201, 201, 201, 201, 201, 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: 712 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052185 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052185 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052185/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052185 Building REAL250005052186 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052186' /scratch/stefan/7921156/working/building/REAL250005052186 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052186 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052186/0 /scratch/stefan/7921156/working/building/REAL250005052186 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/316 `/scratch/stefan/7921156/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCCCCO)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052186.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052186 none CC(CNC(=O)CCCCCO)NC(=O)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', '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, 8, 1, 11, 5, 5, 5, 5, 5, 12, 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, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 18, 34, 34, 34, 117, 139, 167, 182, 200, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 18, 18, 34, 117, 117, 159, 159, 166, 164, 201, 201, 193, 194, 600, 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: 1696 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052186 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052186 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052186/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052186 Building REAL250005052187 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052187' /scratch/stefan/7921156/working/building/REAL250005052187 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052187 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052187/0 /scratch/stefan/7921156/working/building/REAL250005052187 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/317 `/scratch/stefan/7921156/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CSC=N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052187.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052187 none CC(CNC(=O)C1=CSC=N1)NC(=O)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', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [62, 37, 12, 12, 1, 12, 1, 1, 1, 1, 1, 62, 76, 76, 76, 78, 78, 78, 78, 78, 62, 62, 62, 62, 37, 37, 12, 1, 1, 76, 78] 78 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 297 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: REAL250005052187 none CC(CNC(=O)C1=CSC=N1)NC(=O)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', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 32, 60, 60, 60, 78, 78, 78, 78, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 32, 32, 60, 78, 78, 6, 1] 78 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 254 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052187 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052187 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052187/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052187 Building REAL250005052188 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052188' /scratch/stefan/7921156/working/building/REAL250005052188 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052188 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052188/0 /scratch/stefan/7921156/working/building/REAL250005052188 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/318 `/scratch/stefan/7921156/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(CO)CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052188.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052188 none CC(CNC(=O)C1(CO)CCC1)NC(=O)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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [106, 37, 7, 7, 1, 7, 1, 1, 9, 1, 1, 1, 106, 162, 162, 162, 172, 172, 172, 172, 172, 106, 106, 106, 106, 37, 37, 7, 9, 9, 27, 1, 1, 1, 1, 1, 1, 162, 172] 603 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 9, 10, 11, 36, 31] set([0, 1, 2, 3, 5, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38]) total number of confs: 693 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052188 none CC(CNC(=O)C1(CO)CCC1)NC(=O)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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 13, 38, 87, 87, 87, 172, 201, 172, 172, 172, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 38, 38, 87, 201, 201, 603, 172, 172, 172, 172, 172, 172, 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: 1321 number of broken/clashed sets: 103 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052188 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052188 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052188/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052188 Building REAL250005052189 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052189' /scratch/stefan/7921156/working/building/REAL250005052189 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052189 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052189/0 /scratch/stefan/7921156/working/building/REAL250005052189 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/319 `/scratch/stefan/7921156/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCC(N)=O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052189.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052189 none CC(CNC(=O)CCC(N)=O)NC(=O)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.2', 'O.2', 'C.2', 'C.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, 8, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 11, 28, 65, 65, 65, 162, 191, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 28, 28, 65, 162, 162, 191, 191, 201, 201, 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: 827 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052189 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052189 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052189/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052189 Building REAL250005052190 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052190' /scratch/stefan/7921156/working/building/REAL250005052190 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052190 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052190/0 /scratch/stefan/7921156/working/building/REAL250005052190 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/320 `/scratch/stefan/7921156/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005052190.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052190 none C=CCC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 5, 1, 1, 1, 6, 6, 6, 34, 82, 82, 138, 138, 138, 149, 149, 149, 149, 149, 1, 1, 18, 18, 18, 5, 5, 6, 34, 34, 82, 82, 82, 82, 138, 149, 1, 1, 1, 1] 201 rigid atoms, others: [35, 2, 3, 4, 37, 38, 19, 20, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052190 none C=CCC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 75, 75, 75, 32, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 149, 149, 201, 201, 201, 201, 201, 75, 32, 32, 12, 12, 12, 12, 4, 1, 149, 149, 149, 149] 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: 777 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052190 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052190 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052190/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052190 Building REAL250005052191 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052191' /scratch/stefan/7921156/working/building/REAL250005052191 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052191 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052191/0 /scratch/stefan/7921156/working/building/REAL250005052191 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/321 `/scratch/stefan/7921156/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)COC(F)F)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052191.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052191 none CC(CNC(=O)COC(F)F)NC(=O)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', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 15, 15, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 22, 56, 56, 56, 158, 196, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 22, 56, 158, 158, 201, 4, 1] 201 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 683 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052191 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052191 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052191/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052191 Building REAL250005052192 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052192' /scratch/stefan/7921156/working/building/REAL250005052192 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052192 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052192/0 /scratch/stefan/7921156/working/building/REAL250005052192 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/322 `/scratch/stefan/7921156/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052192.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052192 none COC(C)(C)CC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 120, 192, 191, 71, 71, 71, 31, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 193, 193, 193, 193, 193, 193, 120, 120, 71, 31, 31, 13, 13, 13, 13, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 889 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052192 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052192 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052192/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052192 Building REAL250005052193 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052193' /scratch/stefan/7921156/working/building/REAL250005052193 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052193 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052193/0 /scratch/stefan/7921156/working/building/REAL250005052193 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/323 `/scratch/stefan/7921156/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052193.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052193 none CC(O)CCC(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 531 conformations in input total number of sets (complete confs): 531 using faster count positions algorithm for large data unique positions, atoms: [177, 145, 177, 144, 74, 74, 74, 35, 19, 11, 19, 11, 1, 11, 1, 1, 1, 1, 1, 1, 177, 177, 177, 170, 531, 160, 160, 144, 144, 74, 35, 35, 19, 19, 19, 19, 11, 1] 531 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: 1334 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052193 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052193 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052193/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052193 Building REAL250005052194 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052194' /scratch/stefan/7921156/working/building/REAL250005052194 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052194 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052194/0 /scratch/stefan/7921156/working/building/REAL250005052194 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/324 `/scratch/stefan/7921156/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052194.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052194 none C#CCC(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 168, 106, 168, 106, 106, 47, 16, 4, 16, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 168, 168, 168, 168, 106, 47, 47, 16, 16, 16, 16, 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: 841 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052194 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052194 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052194/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052194 Building REAL250005052195 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052195' /scratch/stefan/7921156/working/building/REAL250005052195 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052195 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052195/0 /scratch/stefan/7921156/working/building/REAL250005052195 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/325 `/scratch/stefan/7921156/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)CCO)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052195.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052195 none CC(CNC(=O)C(C)CCO)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 13, 35, 88, 88, 88, 182, 182, 200, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 35, 35, 88, 182, 182, 182, 182, 201, 201, 201, 200, 603, 4, 1] 603 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1421 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052195 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052195 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052195/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052195 Building REAL250005052196 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052196' /scratch/stefan/7921156/working/building/REAL250005052196 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052196 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052196/0 /scratch/stefan/7921156/working/building/REAL250005052196 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/326 `/scratch/stefan/7921156/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(F)=CC1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052196.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052196 none CC(CNC(=O)C(F)=CC1CC1)NC(=O)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', 'F', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 15, 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, 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: [175, 119, 44, 44, 8, 44, 8, 8, 1, 1, 1, 1, 175, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 175, 175, 119, 119, 44, 8, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 798 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: REAL250005052196 none CC(CNC(=O)C(F)=CC1CC1)NC(=O)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', 'F', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 15, 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, 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: [14, 4, 14, 46, 106, 106, 106, 163, 163, 163, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 46, 46, 106, 163, 201, 201, 201, 201, 201, 4, 1] 201 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 683 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052196 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052196 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052196/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052196 Building REAL250005052197 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052197' /scratch/stefan/7921156/working/building/REAL250005052197 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052197 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052197/0 /scratch/stefan/7921156/working/building/REAL250005052197 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/327 `/scratch/stefan/7921156/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CC(F)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052197.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052197 none CC(CNC(=O)CC1CC(F)C1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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: [181, 129, 41, 41, 6, 41, 1, 1, 1, 1, 1, 1, 181, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 181, 129, 129, 41, 6, 6, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 30, 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, 36, 37]) total number of confs: 827 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052197 none CC(CNC(=O)CC1CC(F)C1)NC(=O)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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: [9, 4, 9, 27, 79, 79, 79, 183, 201, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 27, 79, 183, 183, 201, 201, 201, 201, 201, 201, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 795 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052197 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052197 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052197/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052197 Building REAL250005052198 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052198' /scratch/stefan/7921156/working/building/REAL250005052198 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052198 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052198/0 /scratch/stefan/7921156/working/building/REAL250005052198 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/328 `/scratch/stefan/7921156/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H](O)CF)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052198.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052198 none CC(CNC(=O)[C@H](O)CF)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 15, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 43, 102, 102, 102, 189, 189, 189, 201, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 43, 43, 102, 567, 201, 201, 8, 1] 603 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 1375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052198 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052198 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052198/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052198 Building REAL250005052199 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052199' /scratch/stefan/7921156/working/building/REAL250005052199 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052199 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052199/0 /scratch/stefan/7921156/working/building/REAL250005052199 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/329 `/scratch/stefan/7921156/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=NN=CN1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052199.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052199 none CC(CNC(=O)C1=NN=CN1C)NC(=O)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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 8, 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, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [59, 36, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 59, 69, 69, 69, 69, 69, 69, 69, 69, 59, 59, 59, 59, 36, 36, 9, 1, 2, 2, 2, 69, 69] 69 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: 278 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: REAL250005052199 none CC(CNC(=O)C1=NN=CN1C)NC(=O)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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 8, 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, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 27, 59, 59, 59, 69, 69, 69, 69, 69, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 27, 27, 59, 69, 69, 69, 69, 5, 1] 69 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 219 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052199 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052199 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052199/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052199 Building REAL250005052200 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052200' /scratch/stefan/7921156/working/building/REAL250005052200 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052200 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052200/0 /scratch/stefan/7921156/working/building/REAL250005052200 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/330 `/scratch/stefan/7921156/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(O)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052200.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052200 none CC(CNC(=O)C1(O)CC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 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 543 conformations in input total number of sets (complete confs): 543 using faster count positions algorithm for large data unique positions, atoms: [139, 71, 13, 13, 1, 13, 1, 1, 1, 1, 139, 175, 175, 175, 181, 181, 181, 181, 181, 139, 139, 139, 139, 71, 71, 13, 6, 1, 1, 1, 1, 175, 181] 543 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]) total number of confs: 716 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: REAL250005052200 none CC(CNC(=O)C1(O)CC1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 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 543 conformations in input total number of sets (complete confs): 543 using faster count positions algorithm for large data unique positions, atoms: [23, 10, 23, 58, 114, 114, 114, 181, 181, 181, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 58, 58, 114, 543, 181, 181, 181, 181, 10, 1] 543 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: 1158 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052200 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052200 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052200/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052200 Building REAL250005052201 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052201' /scratch/stefan/7921156/working/building/REAL250005052201 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052201 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052201/0 /scratch/stefan/7921156/working/building/REAL250005052201 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/331 `/scratch/stefan/7921156/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC1) `REAL250005052201.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052201 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [62, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 63, 98, 98, 98, 171, 201, 201, 63, 63, 63, 63, 20, 20, 5, 1, 98, 171, 171, 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: 847 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052201 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 25, 80, 144, 201, 201, 201, 201, 201, 201, 201, 201, 25, 3, 25, 1, 1, 1, 1, 80, 80, 80, 80, 144, 144, 201, 201, 25, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 787 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052201 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052201 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052201/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052201 Building REAL250005052202 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052202' /scratch/stefan/7921156/working/building/REAL250005052202 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052202 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052202/0 /scratch/stefan/7921156/working/building/REAL250005052202 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/332 `/scratch/stefan/7921156/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)F) `REAL250005052202.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052202 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 15, 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, 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] 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: [79, 31, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 81, 110, 110, 110, 147, 147, 147, 81, 81, 81, 81, 31, 31, 9, 1, 110, 147, 147, 147, 147, 147, 147] 147 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: 606 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052202 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052202 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052202/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052202 Building REAL250005052203 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052203' /scratch/stefan/7921156/working/building/REAL250005052203 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052203 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052203/0 /scratch/stefan/7921156/working/building/REAL250005052203 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/333 `/scratch/stefan/7921156/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)NC(=O)C(C)(F)F) `REAL250005052203.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052203 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [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] 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: [65, 27, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 66, 99, 99, 99, 161, 161, 161, 66, 66, 66, 66, 27, 27, 10, 1, 99, 161, 161, 161] 161 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]) total number of confs: 669 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052203 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052203 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052203/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052203 Building REAL250005052204 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052204' /scratch/stefan/7921156/working/building/REAL250005052204 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052204 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052204/0 /scratch/stefan/7921156/working/building/REAL250005052204 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/334 `/scratch/stefan/7921156/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052204.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052204 none COCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 130, 130, 130, 87, 32, 85, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 199, 130, 87, 87, 87, 87, 32, 32, 9, 1] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 831 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052204 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052204 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052204/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052204 Building REAL250005052205 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052205' /scratch/stefan/7921156/working/building/REAL250005052205 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052205 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052205/0 /scratch/stefan/7921156/working/building/REAL250005052205 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/335 `/scratch/stefan/7921156/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)NC(=O)C1=CC=CC=N1) `REAL250005052205.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052205 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CC=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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 1, 8, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [67, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 68, 90, 90, 90, 91, 91, 91, 91, 91, 68, 68, 68, 68, 31, 31, 9, 1, 90, 91, 91, 91, 91] 91 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: 356 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052205 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CC=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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 1, 8, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [14, 3, 14, 51, 82, 82, 82, 91, 91, 91, 91, 91, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 51, 51, 82, 91, 3, 1, 1, 1, 1] 91 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052205 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052205 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052205/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052205 Building REAL250005052206 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052206' /scratch/stefan/7921156/working/building/REAL250005052206 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052206 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052206/0 /scratch/stefan/7921156/working/building/REAL250005052206 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/336 `/scratch/stefan/7921156/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NC=C1) `REAL250005052206.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052206 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NC=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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 1, 1, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [76, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 77, 97, 97, 97, 98, 98, 98, 98, 98, 77, 77, 77, 77, 32, 32, 10, 1, 97, 98, 98, 98, 98] 98 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: 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: REAL250005052206 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NC=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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 1, 1, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 12, 50, 89, 89, 89, 98, 98, 98, 98, 98, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 89, 98, 4, 1, 1, 1, 1] 98 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052206 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052206 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052206/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052206 Building REAL250005052207 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052207' /scratch/stefan/7921156/working/building/REAL250005052207 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052207 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052207/0 /scratch/stefan/7921156/working/building/REAL250005052207 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/337 `/scratch/stefan/7921156/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052207.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052207 none CCCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 109, 109, 109, 69, 24, 68, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 195, 195, 109, 69, 69, 69, 69, 24, 24, 6, 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: 849 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052207 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052207 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052207/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052207 Building REAL250005052208 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052208' /scratch/stefan/7921156/working/building/REAL250005052208 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052208 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052208/0 /scratch/stefan/7921156/working/building/REAL250005052208 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/338 `/scratch/stefan/7921156/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CN=C1) `REAL250005052208.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052208 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CN=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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 8, 1, 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, 3, 7, 3, 4, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [65, 24, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 66, 83, 83, 83, 118, 118, 118, 118, 118, 66, 66, 66, 66, 24, 24, 10, 1, 83, 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]) 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: REAL250005052208 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CN=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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 8, 1, 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, 3, 7, 3, 4, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 20, 67, 110, 110, 110, 118, 118, 118, 118, 118, 5, 1, 5, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 67, 67, 110, 118, 5, 1, 1, 1, 1] 118 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 425 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052208 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052208 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052208/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052208 Building REAL250005052209 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052209' /scratch/stefan/7921156/working/building/REAL250005052209 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052209 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052209/0 /scratch/stefan/7921156/working/building/REAL250005052209 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/339 `/scratch/stefan/7921156/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CO1) `REAL250005052209.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052209 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 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: [78, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 78, 94, 94, 94, 101, 101, 101, 101, 78, 78, 78, 78, 33, 33, 9, 1, 94, 101, 101, 101] 101 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]) 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: REAL250005052209 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 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: [21, 6, 21, 55, 93, 93, 93, 101, 101, 101, 101, 101, 6, 1, 6, 1, 1, 1, 1, 1, 21, 21, 21, 21, 55, 55, 93, 101, 6, 1, 1, 1] 101 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052209 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052209 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052209/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052209 Building REAL250005052210 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052210' /scratch/stefan/7921156/working/building/REAL250005052210 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052210 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052210/0 /scratch/stefan/7921156/working/building/REAL250005052210 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/340 `/scratch/stefan/7921156/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052210.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052210 none CC(=O)NCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 108, 77, 77, 77, 47, 17, 46, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 108, 108, 77, 47, 47, 47, 47, 17, 17, 4, 1] 114 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 472 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052210 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052210 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052210/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052210 Building REAL250005052211 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052211' /scratch/stefan/7921156/working/building/REAL250005052211 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052211 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052211/0 /scratch/stefan/7921156/working/building/REAL250005052211 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/341 `/scratch/stefan/7921156/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CC=C1) `REAL250005052211.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052211 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CC=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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 1, 1, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [79, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 80, 103, 103, 103, 105, 105, 103, 105, 105, 80, 80, 80, 80, 30, 30, 9, 1, 103, 105, 105, 105, 105, 105] 105 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: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052211 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CC=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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 1, 1, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 13, 56, 98, 98, 98, 105, 105, 105, 105, 105, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 56, 56, 98, 105, 4, 1, 1, 1, 1, 1] 105 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 358 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052211 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052211 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052211/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052211 Building REAL250005052212 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052212' /scratch/stefan/7921156/working/building/REAL250005052212 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052212 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052212/0 /scratch/stefan/7921156/working/building/REAL250005052212 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/342 `/scratch/stefan/7921156/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052212.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052212 none CC(C)CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [170, 171, 172, 105, 105, 105, 68, 29, 66, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 172, 172, 172, 171, 171, 105, 68, 68, 68, 68, 29, 29, 9, 1] 172 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: 765 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052212 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052212 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052212/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052212 Building REAL250005052213 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052213' /scratch/stefan/7921156/working/building/REAL250005052213 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052213 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052213/0 /scratch/stefan/7921156/working/building/REAL250005052213 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/343 `/scratch/stefan/7921156/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCCC1) `REAL250005052213.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052213 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 24, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 68, 109, 109, 109, 201, 201, 201, 201, 201, 68, 68, 68, 68, 24, 24, 8, 1, 109, 201, 201, 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: 684 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052213 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 12, 48, 131, 194, 194, 194, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 131, 131, 194, 201, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 738 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052213 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052213 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052213/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052213 Building REAL250005052214 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052214' /scratch/stefan/7921156/working/building/REAL250005052214 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052214 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052214/0 /scratch/stefan/7921156/working/building/REAL250005052214 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/344 `/scratch/stefan/7921156/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)NC(=O)C1=CN=CC=N1) `REAL250005052214.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052214 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CC=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.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [67, 35, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 67, 92, 92, 92, 93, 93, 93, 93, 93, 67, 67, 67, 67, 35, 35, 9, 1, 92, 93, 93, 93] 93 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]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052214 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CC=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.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 3, 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: [14, 4, 14, 53, 85, 85, 85, 93, 93, 93, 93, 93, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 53, 53, 85, 93, 4, 1, 1, 1] 93 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 326 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052214 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052214 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052214/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052214 Building REAL250005052215 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052215' /scratch/stefan/7921156/working/building/REAL250005052215 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052215 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052215/0 /scratch/stefan/7921156/working/building/REAL250005052215 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/345 `/scratch/stefan/7921156/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CCCC1) `REAL250005052215.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052215 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 52, 71, 71, 71, 185, 201, 201, 201, 201, 52, 52, 52, 52, 21, 21, 4, 1, 71, 185, 185, 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: 799 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052215 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 34, 83, 154, 201, 201, 201, 201, 201, 201, 201, 201, 34, 6, 34, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 154, 154, 201, 201, 34, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 798 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052215 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052215 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052215/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052215 Building REAL250005052216 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052216' /scratch/stefan/7921156/working/building/REAL250005052216 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052216 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052216/0 /scratch/stefan/7921156/working/building/REAL250005052216 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/346 `/scratch/stefan/7921156/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)NC(=O)C1=CC=CS1) `REAL250005052216.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052216 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [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] 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: [68, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 70, 100, 100, 100, 120, 120, 120, 120, 70, 70, 70, 70, 32, 32, 10, 1, 100, 120, 120, 120] 120 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]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052216 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [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] 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: [26, 8, 26, 65, 112, 112, 112, 120, 120, 120, 120, 120, 9, 1, 9, 1, 1, 1, 1, 1, 26, 26, 26, 26, 65, 65, 112, 120, 9, 1, 1, 1] 120 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052216 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052216 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052216/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052216 Building REAL250005052217 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052217' /scratch/stefan/7921156/working/building/REAL250005052217 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052217 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052217/0 /scratch/stefan/7921156/working/building/REAL250005052217 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/347 `/scratch/stefan/7921156/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1C) `REAL250005052217.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052217 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [77, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 78, 113, 113, 113, 201, 201, 201, 78, 78, 78, 78, 31, 31, 10, 1, 113, 201, 201, 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: 703 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052217 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [48, 13, 48, 126, 189, 189, 189, 201, 201, 201, 201, 201, 13, 1, 13, 1, 1, 1, 1, 48, 48, 48, 48, 126, 126, 189, 201, 13, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 732 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052217 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052217 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052217/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052217 Building REAL250005052218 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052218' /scratch/stefan/7921156/working/building/REAL250005052218 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052218 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052218/0 /scratch/stefan/7921156/working/building/REAL250005052218 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/348 `/scratch/stefan/7921156/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052218.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052218 none CCOCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 175, 123, 123, 123, 71, 20, 69, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 175, 175, 123, 71, 71, 71, 71, 20, 20, 4, 1] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 803 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052218 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052218 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052218/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052218 Building REAL250005052219 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052219' /scratch/stefan/7921156/working/building/REAL250005052219 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052219 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052219/0 /scratch/stefan/7921156/working/building/REAL250005052219 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/349 `/scratch/stefan/7921156/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052219.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052219 none CC(C)=CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 107, 107, 107, 72, 32, 71, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 139, 139, 139, 107, 72, 72, 72, 72, 32, 32, 10, 1] 139 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: 516 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052219 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052219 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052219/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052219 Building REAL250005052220 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052220' /scratch/stefan/7921156/working/building/REAL250005052220 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052220 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052220/0 /scratch/stefan/7921156/working/building/REAL250005052220 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/350 `/scratch/stefan/7921156/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COCCO1) `REAL250005052220.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052220 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [62, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 62, 84, 84, 84, 88, 88, 88, 88, 88, 62, 62, 62, 62, 28, 28, 9, 1, 84, 88, 88, 88, 88, 88] 88 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: 317 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: REAL250005052220 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 17, 46, 81, 81, 81, 88, 88, 88, 88, 88, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 46, 46, 81, 88, 7, 1, 1, 1, 1, 1] 88 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 293 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052220 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052220 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052220/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052220 Building REAL250005052221 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052221' /scratch/stefan/7921156/working/building/REAL250005052221 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052221 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052221/0 /scratch/stefan/7921156/working/building/REAL250005052221 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/351 `/scratch/stefan/7921156/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052221.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052221 none CC(=O)NC(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 117, 77, 117, 77, 77, 48, 16, 46, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 117, 117, 117, 117, 77, 48, 48, 48, 48, 16, 16, 4, 1] 118 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: 508 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052221 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052221 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052221/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052221 Building REAL250005052222 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052222' /scratch/stefan/7921156/working/building/REAL250005052222 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052222 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052222/0 /scratch/stefan/7921156/working/building/REAL250005052222 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/352 `/scratch/stefan/7921156/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005052222.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052222 none CC1=CC=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 21, 21, 59, 102, 102, 102, 110, 110, 110, 110, 110, 1, 2, 2, 2, 1, 1, 6, 21, 21, 21, 21, 59, 59, 102, 110] 110 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052222 none CC1=CC=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 100, 100, 100, 67, 31, 67, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 110, 110, 100, 67, 67, 67, 67, 31, 31, 10, 1] 110 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: 387 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052222 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052222 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052222/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052222 Building REAL250005052223 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052223' /scratch/stefan/7921156/working/building/REAL250005052223 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052223 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052223/0 /scratch/stefan/7921156/working/building/REAL250005052223 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/353 `/scratch/stefan/7921156/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCO1) `REAL250005052223.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052223 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [90, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 91, 132, 132, 132, 167, 167, 167, 167, 91, 91, 91, 91, 36, 36, 11, 1, 132, 167, 167, 167, 167, 167, 167, 167] 167 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: 612 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052223 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [38, 10, 38, 105, 153, 153, 153, 167, 167, 167, 167, 167, 10, 1, 10, 1, 1, 1, 1, 1, 38, 38, 38, 38, 105, 105, 153, 167, 10, 1, 1, 1, 1, 1, 1, 1] 167 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 597 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052223 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052223 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052223/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052223 Building REAL250005052224 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052224' /scratch/stefan/7921156/working/building/REAL250005052224 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052224 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052224/0 /scratch/stefan/7921156/working/building/REAL250005052224 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/354 `/scratch/stefan/7921156/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052224.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052224 none CSCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 105, 105, 105, 68, 24, 66, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 182, 182, 105, 68, 68, 68, 68, 24, 24, 8, 1] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 809 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052224 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052224 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052224/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052224 Building REAL250005052225 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052225' /scratch/stefan/7921156/working/building/REAL250005052225 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052225 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052225/0 /scratch/stefan/7921156/working/building/REAL250005052225 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/355 `/scratch/stefan/7921156/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=NO1) `REAL250005052225.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052225 none CC1=CC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 57, 99, 99, 99, 104, 104, 104, 104, 104, 1, 1, 2, 2, 2, 1, 5, 18, 18, 18, 18, 57, 57, 99, 104] 104 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 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: REAL250005052225 none CC1=CC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 101, 101, 101, 71, 34, 71, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 104, 101, 71, 71, 71, 71, 34, 34, 9, 1] 104 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: 380 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052225 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052225 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052225/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052225 Building REAL250005052226 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052226' /scratch/stefan/7921156/working/building/REAL250005052226 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052226 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052226/0 /scratch/stefan/7921156/working/building/REAL250005052226 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/356 `/scratch/stefan/7921156/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052226.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052226 none CSCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 165, 86, 86, 86, 59, 24, 59, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 171, 171, 165, 165, 86, 59, 59, 59, 59, 24, 24, 8, 1] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 775 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052226 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052226 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052226/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052226 Building REAL250005052227 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052227' /scratch/stefan/7921156/working/building/REAL250005052227 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052227 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052227/0 /scratch/stefan/7921156/working/building/REAL250005052227 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/357 `/scratch/stefan/7921156/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052227.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052227 none CC(C)CCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 194, 201, 183, 84, 84, 84, 50, 17, 50, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 198, 201, 201, 201, 201, 194, 194, 183, 183, 84, 50, 50, 50, 50, 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: 855 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052227 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052227 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052227/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052227 Building REAL250005052228 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052228' /scratch/stefan/7921156/working/building/REAL250005052228 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052228 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052228/0 /scratch/stefan/7921156/working/building/REAL250005052228 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/358 `/scratch/stefan/7921156/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)NC(=O)C1=CSC=C1) `REAL250005052228.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052228 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSC=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.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [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] 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: [62, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 63, 94, 94, 94, 145, 145, 145, 145, 63, 63, 63, 63, 20, 20, 9, 1, 94, 145, 145, 145] 145 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]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052228 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSC=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.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [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] 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: [22, 5, 22, 84, 138, 138, 138, 145, 145, 145, 145, 145, 5, 1, 5, 1, 1, 1, 1, 1, 22, 22, 22, 22, 84, 84, 138, 145, 5, 1, 1, 1] 145 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 525 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052228 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052228 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052228/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052228 Building REAL250005052229 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052229' /scratch/stefan/7921156/working/building/REAL250005052229 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052229 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052229/0 /scratch/stefan/7921156/working/building/REAL250005052229 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/359 `/scratch/stefan/7921156/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C=CO1) `REAL250005052229.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052229 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 35, 35, 97, 148, 148, 148, 153, 153, 153, 153, 153, 1, 1, 1, 2, 2, 2, 9, 35, 35, 35, 35, 97, 97, 148, 153, 1, 1] 153 rigid atoms, others: [0, 1, 2, 3, 33, 34, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052229 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 102, 102, 102, 68, 28, 66, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 153, 153, 102, 68, 68, 68, 68, 28, 28, 9, 1, 153, 153] 153 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 470 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052229 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052229 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052229/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052229 Building REAL250005052230 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052230' /scratch/stefan/7921156/working/building/REAL250005052230 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052230 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052230/0 /scratch/stefan/7921156/working/building/REAL250005052230 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/360 `/scratch/stefan/7921156/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1C=CCC1) `REAL250005052230.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052230 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1C=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.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 1, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 53, 83, 83, 83, 185, 201, 201, 201, 201, 53, 53, 53, 53, 19, 19, 5, 1, 83, 185, 185, 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: 801 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: REAL250005052230 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1C=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.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 1, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 33, 81, 157, 201, 201, 201, 201, 201, 201, 201, 201, 33, 8, 33, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 157, 157, 201, 201, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 819 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052230 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052230 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052230/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052230 Building REAL250005052231 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052231' /scratch/stefan/7921156/working/building/REAL250005052231 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052231 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052231/0 /scratch/stefan/7921156/working/building/REAL250005052231 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/361 `/scratch/stefan/7921156/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NN=N1) `REAL250005052231.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052231 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NN=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [58, 24, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 58, 89, 89, 89, 169, 200, 200, 200, 200, 58, 58, 58, 58, 24, 24, 10, 1, 89, 169, 169, 200] 200 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]) total number of confs: 752 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052231 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NN=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [84, 43, 84, 146, 181, 181, 181, 200, 200, 200, 200, 200, 43, 9, 43, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 146, 146, 181, 200, 43, 9, 9, 1] 200 rigid atoms, others: [32, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 761 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052231 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052231 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052231/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052231 Building REAL250005052232 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052232' /scratch/stefan/7921156/working/building/REAL250005052232 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052232 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052232/0 /scratch/stefan/7921156/working/building/REAL250005052232 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/362 `/scratch/stefan/7921156/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN(C)N=C1) `REAL250005052232.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052232 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN(C)N=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.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 5, 8, 1, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [70, 26, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 71, 90, 90, 90, 122, 122, 122, 122, 122, 71, 71, 71, 71, 26, 26, 10, 1, 90, 122, 122, 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: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052232 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN(C)N=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.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 5, 8, 1, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 20, 72, 116, 116, 116, 122, 122, 122, 122, 122, 5, 1, 5, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 72, 72, 116, 122, 5, 1, 2, 2, 2, 1] 122 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 442 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052232 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052232 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052232/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052232 Building REAL250005052233 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052233' /scratch/stefan/7921156/working/building/REAL250005052233 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052233 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052233/0 /scratch/stefan/7921156/working/building/REAL250005052233 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/363 `/scratch/stefan/7921156/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)NC(=O)C1CC=CCC1) `REAL250005052233.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052233 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC=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.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 1, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 82, 128, 128, 128, 201, 201, 201, 201, 201, 82, 82, 82, 82, 29, 29, 9, 1, 128, 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]) total number of confs: 712 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: REAL250005052233 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC=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.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 1, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 13, 47, 127, 190, 190, 190, 201, 201, 201, 201, 201, 13, 1, 13, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 127, 127, 190, 201, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 722 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052233 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052233 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052233/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052233 Building REAL250005052234 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052234' /scratch/stefan/7921156/working/building/REAL250005052234 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052234 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052234/0 /scratch/stefan/7921156/working/building/REAL250005052234 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/364 `/scratch/stefan/7921156/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005052234.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052234 none CC1=NOC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 60, 95, 95, 95, 97, 97, 97, 97, 97, 1, 2, 2, 2, 7, 19, 19, 19, 19, 60, 60, 95, 97, 1] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 20] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 356 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052234 none CC1=NOC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 97, 89, 89, 89, 65, 26, 64, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 89, 65, 65, 65, 65, 26, 26, 8, 1, 97] 97 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 345 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052234 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052234 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052234/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052234 Building REAL250005052235 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052235' /scratch/stefan/7921156/working/building/REAL250005052235 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052235 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052235/0 /scratch/stefan/7921156/working/building/REAL250005052235 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/365 `/scratch/stefan/7921156/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CN1) `REAL250005052235.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052235 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 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: [63, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 63, 81, 81, 81, 88, 88, 88, 88, 63, 63, 63, 63, 27, 27, 9, 1, 81, 88, 88, 88, 88] 88 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]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052235 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 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: [22, 6, 22, 55, 83, 83, 83, 88, 88, 88, 88, 88, 6, 1, 6, 1, 1, 1, 1, 1, 22, 22, 22, 22, 55, 55, 83, 88, 6, 1, 1, 1, 1] 88 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052235 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052235 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052235/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052235 Building REAL250005052236 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052236' /scratch/stefan/7921156/working/building/REAL250005052236 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052236 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052236/0 /scratch/stefan/7921156/working/building/REAL250005052236 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/366 `/scratch/stefan/7921156/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)CCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052236.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052236 none CC(=O)CCCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 160, 201, 92, 85, 30, 30, 30, 22, 12, 22, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 154, 147, 113, 113, 85, 85, 30, 22, 22, 22, 22, 12, 12, 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: 961 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052236 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052236 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052236/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052236 Building REAL250005052237 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052237' /scratch/stefan/7921156/working/building/REAL250005052237 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052237 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052237/0 /scratch/stefan/7921156/working/building/REAL250005052237 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/367 `/scratch/stefan/7921156/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COC=C1) `REAL250005052237.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052237 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [60, 23, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 61, 89, 89, 89, 139, 139, 139, 139, 61, 61, 61, 61, 23, 23, 10, 1, 89, 139, 139, 139] 139 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]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052237 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [21, 5, 21, 77, 129, 129, 129, 139, 139, 139, 139, 139, 5, 1, 5, 1, 1, 1, 1, 1, 21, 21, 21, 21, 77, 77, 129, 139, 5, 1, 1, 1] 139 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 496 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052237 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052237 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052237/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052237 Building REAL250005052238 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052238' /scratch/stefan/7921156/working/building/REAL250005052238 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052238 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052238/0 /scratch/stefan/7921156/working/building/REAL250005052238 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/368 `/scratch/stefan/7921156/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)NC(=O)CN1C=CC=N1) `REAL250005052238.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052238 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=CC=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 1, 1, 8, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 53, 84, 84, 84, 163, 201, 201, 201, 201, 53, 53, 53, 53, 20, 20, 5, 1, 84, 163, 163, 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: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052238 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=CC=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 1, 1, 8, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 45, 87, 165, 199, 199, 199, 201, 201, 201, 201, 201, 45, 9, 45, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 165, 165, 199, 201, 45, 9, 9, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 797 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052238 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052238 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052238/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052238 Building REAL250005052239 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052239' /scratch/stefan/7921156/working/building/REAL250005052239 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052239 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052239/0 /scratch/stefan/7921156/working/building/REAL250005052239 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/369 `/scratch/stefan/7921156/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)OC=C1) `REAL250005052239.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052239 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 34, 34, 96, 148, 148, 148, 161, 161, 161, 161, 161, 1, 1, 1, 2, 2, 2, 9, 34, 34, 34, 34, 96, 96, 148, 161, 1, 1] 161 rigid atoms, others: [0, 1, 2, 3, 33, 34, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 567 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: REAL250005052239 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 126, 126, 126, 88, 34, 88, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 161, 161, 126, 88, 88, 88, 88, 34, 34, 9, 1, 161, 161] 161 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 529 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052239 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052239 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052239/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052239 Building REAL250005052240 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052240' /scratch/stefan/7921156/working/building/REAL250005052240 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052240 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052240/0 /scratch/stefan/7921156/working/building/REAL250005052240 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/370 `/scratch/stefan/7921156/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052240.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052240 none CCCCCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 190, 167, 129, 44, 44, 44, 37, 16, 37, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 201, 201, 201, 201, 191, 190, 172, 172, 129, 129, 44, 37, 37, 37, 37, 16, 16, 4, 1] 201 rigid atoms, others: [39, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 940 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052240 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052240 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052240/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052240 Building REAL250005052241 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052241' /scratch/stefan/7921156/working/building/REAL250005052241 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052241 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052241/0 /scratch/stefan/7921156/working/building/REAL250005052241 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/371 `/scratch/stefan/7921156/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(C)(C)C) `REAL250005052241.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052241 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [59, 27, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 61, 94, 94, 94, 117, 117, 117, 117, 61, 61, 61, 61, 27, 27, 9, 1, 94, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117] 117 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: 492 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052241 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052241 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052241/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052241 Building REAL250005052242 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052242' /scratch/stefan/7921156/working/building/REAL250005052242 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052242 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052242/0 /scratch/stefan/7921156/working/building/REAL250005052242 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/372 `/scratch/stefan/7921156/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)NC(=O)C1=CC=CN1C) `REAL250005052242.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052242 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [68, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 100, 100, 100, 108, 108, 108, 108, 108, 69, 69, 69, 69, 26, 26, 9, 1, 100, 108, 108, 108, 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, 35]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052242 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 21, 57, 103, 103, 103, 108, 108, 108, 108, 108, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 57, 57, 103, 108, 7, 1, 1, 1, 2, 2, 2] 108 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 387 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052242 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052242 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052242/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052242 Building REAL250005052243 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052243' /scratch/stefan/7921156/working/building/REAL250005052243 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052243 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052243/0 /scratch/stefan/7921156/working/building/REAL250005052243 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/373 `/scratch/stefan/7921156/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052243.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052243 none CCCCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 188, 175, 76, 76, 76, 41, 14, 41, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 201, 201, 201, 201, 188, 188, 175, 175, 76, 41, 41, 41, 41, 14, 14, 4, 1] 201 rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 849 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052243 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052243 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052243/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052243 Building REAL250005052244 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052244' /scratch/stefan/7921156/working/building/REAL250005052244 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052244 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052244/0 /scratch/stefan/7921156/working/building/REAL250005052244 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/374 `/scratch/stefan/7921156/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052244.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052244 none CC(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [168, 114, 168, 114, 114, 78, 34, 76, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 168, 168, 168, 114, 78, 78, 78, 78, 34, 34, 10, 1] 168 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: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052244 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052244 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052244/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052244 Building REAL250005052245 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052245' /scratch/stefan/7921156/working/building/REAL250005052245 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052245 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052245/0 /scratch/stefan/7921156/working/building/REAL250005052245 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/375 `/scratch/stefan/7921156/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052245.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052245 none CCC(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 111, 185, 111, 111, 74, 28, 71, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 185, 185, 185, 185, 111, 74, 74, 74, 74, 28, 28, 9, 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: 879 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052245 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052245 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052245/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052245 Building REAL250005052246 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052246' /scratch/stefan/7921156/working/building/REAL250005052246 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052246 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052246/0 /scratch/stefan/7921156/working/building/REAL250005052246 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/376 `/scratch/stefan/7921156/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)NC(=O)CSCC#N) `REAL250005052246.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052246 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CSCC#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.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 14, 5, 1, 8, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 53, 53, 53, 112, 179, 201, 201, 39, 39, 39, 39, 16, 16, 4, 1, 53, 112, 112, 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]) total number of confs: 689 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052246 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052246 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052246/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052246 Building REAL250005052247 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052247' /scratch/stefan/7921156/working/building/REAL250005052247 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052247 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052247/0 /scratch/stefan/7921156/working/building/REAL250005052247 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/377 `/scratch/stefan/7921156/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052247.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052247 none CC(=O)N(C)CC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 94, 105, 70, 70, 70, 46, 17, 45, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 105, 94, 94, 70, 46, 46, 46, 46, 17, 17, 4, 1] 105 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: 443 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052247 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052247 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052247/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052247 Building REAL250005052248 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052248' /scratch/stefan/7921156/working/building/REAL250005052248 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052248 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052248/0 /scratch/stefan/7921156/working/building/REAL250005052248 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/378 `/scratch/stefan/7921156/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052248.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052248 none CCC(CC)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [175, 151, 111, 151, 173, 111, 111, 75, 31, 73, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 176, 176, 176, 176, 176, 151, 173, 173, 173, 173, 173, 111, 75, 75, 75, 75, 31, 31, 9, 1] 187 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: 926 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052248 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052248 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052248/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052248 Building REAL250005052249 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052249' /scratch/stefan/7921156/working/building/REAL250005052249 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052249 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052249/0 /scratch/stefan/7921156/working/building/REAL250005052249 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/379 `/scratch/stefan/7921156/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052249.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052249 none CC(C)OCCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 151, 201, 129, 117, 51, 51, 51, 36, 11, 36, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 129, 129, 117, 117, 51, 36, 36, 36, 36, 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: 877 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052249 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052249 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052249/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052249 Building REAL250005052250 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052250' /scratch/stefan/7921156/working/building/REAL250005052250 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052250 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052250/0 /scratch/stefan/7921156/working/building/REAL250005052250 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/380 `/scratch/stefan/7921156/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COCCO1) `REAL250005052250.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052250 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COCCO1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [85, 35, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 85, 133, 133, 133, 171, 171, 171, 171, 171, 85, 85, 85, 85, 35, 35, 9, 1, 133, 171, 171, 171, 171, 171, 171, 171] 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]) total number of confs: 623 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052250 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COCCO1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [36, 10, 36, 109, 163, 163, 163, 171, 171, 171, 171, 171, 10, 1, 10, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 109, 109, 163, 171, 10, 1, 1, 1, 1, 1, 1, 1] 171 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 618 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052250 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052250 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052250/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052250 Building REAL250005052251 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052251' /scratch/stefan/7921156/working/building/REAL250005052251 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052251 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052251/0 /scratch/stefan/7921156/working/building/REAL250005052251 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/381 `/scratch/stefan/7921156/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NN1) `REAL250005052251.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052251 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 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: [47, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 47, 58, 58, 58, 65, 65, 65, 65, 47, 47, 47, 47, 21, 21, 9, 1, 58, 65, 65, 65] 65 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]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052251 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 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: [18, 7, 18, 42, 60, 60, 60, 65, 65, 65, 65, 65, 7, 1, 7, 1, 1, 1, 1, 1, 18, 18, 18, 18, 42, 42, 60, 65, 7, 1, 1, 1] 65 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052251 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052251 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052251/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052251 Building REAL250005052252 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052252' /scratch/stefan/7921156/working/building/REAL250005052252 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052252 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052252/0 /scratch/stefan/7921156/working/building/REAL250005052252 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/382 `/scratch/stefan/7921156/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052252.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052252 none CSC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 100, 174, 100, 100, 62, 18, 60, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 174, 174, 174, 174, 100, 62, 62, 62, 62, 18, 18, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052252 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052252 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052252/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052252 Building REAL250005052253 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052253' /scratch/stefan/7921156/working/building/REAL250005052253 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052253 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052253/0 /scratch/stefan/7921156/working/building/REAL250005052253 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/383 `/scratch/stefan/7921156/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052253.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052253 none CCOC(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 192, 143, 192, 143, 143, 83, 27, 80, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 192, 192, 192, 192, 143, 83, 83, 83, 83, 27, 27, 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: 826 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052253 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052253 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052253/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052253 Building REAL250005052254 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052254' /scratch/stefan/7921156/working/building/REAL250005052254 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052254 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052254/0 /scratch/stefan/7921156/working/building/REAL250005052254 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/384 `/scratch/stefan/7921156/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052254.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052254 none CCOCCCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 190, 101, 101, 24, 24, 24, 13, 10, 13, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 176, 166, 133, 133, 101, 101, 24, 13, 13, 13, 13, 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: 976 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052254 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052254 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052254/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052254 Building REAL250005052255 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052255' /scratch/stefan/7921156/working/building/REAL250005052255 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052255 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052255/0 /scratch/stefan/7921156/working/building/REAL250005052255 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/385 `/scratch/stefan/7921156/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)NC(=O)COCC1CC1) `REAL250005052255.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052255 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COCC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 25, 25, 25, 58, 103, 144, 201, 201, 20, 20, 20, 20, 8, 8, 2, 1, 25, 58, 58, 144, 144, 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: 758 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052255 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COCC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 100, 137, 164, 201, 201, 201, 201, 201, 201, 201, 201, 100, 54, 100, 23, 8, 1, 1, 1, 1, 137, 137, 137, 137, 164, 164, 201, 201, 100, 54, 54, 8, 8, 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: 828 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052255 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052255 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052255/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052255 Building REAL250005052256 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052256' /scratch/stefan/7921156/working/building/REAL250005052256 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052256 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052256/0 /scratch/stefan/7921156/working/building/REAL250005052256 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/386 `/scratch/stefan/7921156/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)NC(=O)CC1CCCO1) `REAL250005052256.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052256 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 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, 7] 0 hydrogens 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, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 58, 95, 95, 95, 176, 201, 201, 201, 201, 58, 58, 58, 58, 21, 21, 6, 1, 95, 176, 176, 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: 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: REAL250005052256 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 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, 7] 0 hydrogens 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, 36, 85, 160, 199, 199, 199, 201, 201, 201, 201, 201, 36, 7, 36, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 160, 160, 199, 201, 36, 7, 7, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 786 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052256 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052256 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052256/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052256 Building REAL250005052257 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052257' /scratch/stefan/7921156/working/building/REAL250005052257 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052257 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052257/0 /scratch/stefan/7921156/working/building/REAL250005052257 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/387 `/scratch/stefan/7921156/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNN=C1) `REAL250005052257.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052257 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7] dock color type numbers: [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] 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: [62, 29, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 62, 81, 81, 81, 81, 81, 81, 81, 62, 62, 62, 62, 29, 29, 11, 1, 81, 81, 81, 81] 81 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]) total number of confs: 297 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: REAL250005052257 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7] dock color type numbers: [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] 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: [13, 4, 13, 38, 62, 62, 62, 68, 68, 68, 68, 68, 4, 1, 4, 1, 1, 1, 1, 1, 13, 13, 13, 13, 38, 38, 62, 68, 4, 1, 1, 1] 68 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052257 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052257 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052257/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052257 Building REAL250005052258 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052258' /scratch/stefan/7921156/working/building/REAL250005052258 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052258 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052258/0 /scratch/stefan/7921156/working/building/REAL250005052258 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/388 `/scratch/stefan/7921156/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052258.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052258 none COCCCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 133, 63, 63, 63, 39, 18, 39, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 187, 175, 149, 149, 133, 133, 63, 39, 39, 39, 39, 18, 18, 6, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1007 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052258 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052258 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052258/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052258 Building REAL250005052259 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052259' /scratch/stefan/7921156/working/building/REAL250005052259 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052259 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052259/0 /scratch/stefan/7921156/working/building/REAL250005052259 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/389 `/scratch/stefan/7921156/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052259.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052259 none CCOC1CC1C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 32, 76, 143, 143, 143, 152, 152, 152, 152, 152, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 32, 32, 32, 32, 76, 76, 143, 152] 201 rigid atoms, others: [2, 3, 4, 5, 6, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 568 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: REAL250005052259 none CCOC1CC1C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 152, 152, 152, 56, 56, 56, 35, 13, 35, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 152, 152, 152, 152, 56, 35, 35, 35, 35, 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: 565 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052259 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052259 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052259/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052259 Building REAL250005052260 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052260' /scratch/stefan/7921156/working/building/REAL250005052260 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052260 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052260/0 /scratch/stefan/7921156/working/building/REAL250005052260 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/390 `/scratch/stefan/7921156/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)NC(=O)C1=NSN=C1) `REAL250005052260.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052260 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NSN=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.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 14, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [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] 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: [71, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 72, 96, 96, 96, 97, 97, 97, 97, 72, 72, 72, 72, 31, 31, 9, 1, 96, 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]) 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: REAL250005052260 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NSN=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.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 14, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [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] 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: [16, 5, 16, 49, 93, 93, 93, 97, 97, 97, 97, 97, 5, 1, 5, 1, 1, 1, 1, 1, 16, 16, 16, 16, 49, 49, 93, 97, 5, 1] 97 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052260 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052260 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052260/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052260 Building REAL250005052261 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052261' /scratch/stefan/7921156/working/building/REAL250005052261 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052261 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052261/0 /scratch/stefan/7921156/working/building/REAL250005052261 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/391 `/scratch/stefan/7921156/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=NS1) `REAL250005052261.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052261 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'H', 'H', '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, 1, 11, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [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] 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: [46, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 46, 66, 66, 66, 88, 88, 88, 88, 46, 46, 46, 46, 19, 19, 8, 1, 66, 88] 88 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]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052261 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'H', 'H', '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, 1, 11, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [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] 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: [24, 7, 24, 51, 85, 85, 85, 88, 88, 88, 88, 88, 7, 1, 7, 1, 1, 1, 1, 1, 24, 24, 24, 24, 51, 51, 85, 88, 7, 1] 88 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052261 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052261 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052261/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052261 Building REAL250005052262 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052262' /scratch/stefan/7921156/working/building/REAL250005052262 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052262 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052262/0 /scratch/stefan/7921156/working/building/REAL250005052262 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/392 `/scratch/stefan/7921156/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)NC(=O)C1=NOC=C1) `REAL250005052262.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052262 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [69, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 91, 91, 91, 96, 96, 96, 96, 69, 69, 69, 69, 33, 33, 9, 1, 91, 96, 96] 96 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]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052262 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 56, 89, 89, 89, 96, 96, 96, 96, 96, 6, 1, 6, 1, 1, 1, 1, 1, 19, 19, 19, 19, 56, 56, 89, 96, 6, 1, 1] 96 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052262 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052262 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052262/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052262 Building REAL250005052263 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052263' /scratch/stefan/7921156/working/building/REAL250005052263 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052263 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052263/0 /scratch/stefan/7921156/working/building/REAL250005052263 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/393 `/scratch/stefan/7921156/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005052263.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052263 none CC(=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 79, 79, 79, 50, 17, 50, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 148, 201, 201, 148, 148, 148, 148, 79, 50, 50, 50, 50, 17, 17, 4, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 699 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: REAL250005052263 none CC(=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 35, 35, 35, 77, 77, 151, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 8, 8, 8, 8, 35, 77, 77, 77, 77, 151, 151, 201, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 38, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 779 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052263 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052263 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052263/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052263 Building REAL250005052264 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052264' /scratch/stefan/7921156/working/building/REAL250005052264 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052264 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052264/0 /scratch/stefan/7921156/working/building/REAL250005052264 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/394 `/scratch/stefan/7921156/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005052264.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052264 none CC1=NNC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 47, 73, 73, 73, 77, 77, 77, 77, 77, 1, 2, 2, 2, 1, 7, 18, 18, 18, 18, 47, 47, 73, 77, 1] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052264 none CC1=NNC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 71, 71, 71, 45, 18, 45, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 71, 45, 45, 45, 45, 18, 18, 9, 1, 77] 77 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052264 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052264 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052264/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052264 Building REAL250005052265 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052265' /scratch/stefan/7921156/working/building/REAL250005052265 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052265 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052265/0 /scratch/stefan/7921156/working/building/REAL250005052265 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/395 `/scratch/stefan/7921156/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)NC(=O)C1=CN=CS1) `REAL250005052265.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052265 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', '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, 1, 11, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [56, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 56, 81, 81, 81, 95, 95, 95, 95, 56, 56, 56, 56, 23, 23, 9, 1, 81, 95, 95] 95 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]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052265 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', '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, 1, 11, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [23, 8, 23, 52, 91, 91, 91, 95, 95, 95, 95, 95, 8, 1, 8, 1, 1, 1, 1, 1, 23, 23, 23, 23, 52, 52, 91, 95, 9, 1, 1] 95 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 345 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052265 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052265 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052265/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052265 Building REAL250005052266 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052266' /scratch/stefan/7921156/working/building/REAL250005052266 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052266 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052266/0 /scratch/stefan/7921156/working/building/REAL250005052266 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/396 `/scratch/stefan/7921156/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052266.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052266 none CCC=C(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 195, 83, 195, 83, 83, 50, 16, 50, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 195, 195, 195, 195, 83, 50, 50, 50, 50, 16, 16, 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: 653 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052266 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052266 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052266/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052266 Building REAL250005052267 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052267' /scratch/stefan/7921156/working/building/REAL250005052267 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052267 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052267/0 /scratch/stefan/7921156/working/building/REAL250005052267 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/397 `/scratch/stefan/7921156/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)N=CO1) `REAL250005052267.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052267 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 26, 26, 83, 131, 131, 131, 138, 138, 138, 138, 138, 1, 1, 1, 2, 2, 2, 8, 26, 26, 26, 26, 83, 83, 131, 138, 1] 138 rigid atoms, others: [0, 1, 2, 3, 33, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 500 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: REAL250005052267 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 122, 122, 122, 83, 35, 82, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 138, 138, 122, 83, 83, 83, 83, 35, 35, 9, 1, 138] 138 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 490 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052267 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052267 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052267/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052267 Building REAL250005052268 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052268' /scratch/stefan/7921156/working/building/REAL250005052268 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052268 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052268/0 /scratch/stefan/7921156/working/building/REAL250005052268 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/398 `/scratch/stefan/7921156/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(CC)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052268.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052268 none CCOC(CC)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 156, 111, 156, 190, 111, 111, 61, 19, 60, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 156, 199, 199, 199, 199, 199, 111, 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: 982 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052268 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052268 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052268/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052268 Building REAL250005052269 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052269' /scratch/stefan/7921156/working/building/REAL250005052269 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052269 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052269/0 /scratch/stefan/7921156/working/building/REAL250005052269 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/399 `/scratch/stefan/7921156/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(F)(F)F) `REAL250005052269.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052269 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(F)(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.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [70, 30, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 72, 96, 96, 96, 161, 161, 161, 161, 72, 72, 72, 72, 30, 30, 11, 1, 96, 161, 161] 161 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]) total number of confs: 681 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052269 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052269 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052269/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052269 Building REAL250005052270 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052270' /scratch/stefan/7921156/working/building/REAL250005052270 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052270 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052270/0 /scratch/stefan/7921156/working/building/REAL250005052270 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/400 `/scratch/stefan/7921156/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052270.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052270 none COC(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 162, 129, 163, 129, 129, 84, 32, 81, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 165, 165, 165, 163, 163, 163, 163, 129, 84, 84, 84, 84, 32, 32, 9, 1] 165 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: 662 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052270 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052270 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052270/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052270 Building REAL250005052271 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052271' /scratch/stefan/7921156/working/building/REAL250005052271 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052271 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052271/0 /scratch/stefan/7921156/working/building/REAL250005052271 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/401 `/scratch/stefan/7921156/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052271.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052271 none CC(C)OCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 178, 201, 151, 97, 97, 97, 58, 18, 56, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 151, 151, 97, 58, 58, 58, 58, 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: 831 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052271 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052271 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052271/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052271 Building REAL250005052272 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052272' /scratch/stefan/7921156/working/building/REAL250005052272 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052272 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052272/0 /scratch/stefan/7921156/working/building/REAL250005052272 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/402 `/scratch/stefan/7921156/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052272.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052272 none CCCOCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 155, 129, 77, 42, 42, 42, 27, 8, 27, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 155, 155, 77, 77, 42, 27, 27, 27, 27, 8, 8, 2, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 827 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052272 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052272 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052272/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052272 Building REAL250005052273 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052273' /scratch/stefan/7921156/working/building/REAL250005052273 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052273 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052273/0 /scratch/stefan/7921156/working/building/REAL250005052273 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/403 `/scratch/stefan/7921156/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCOC1) `REAL250005052273.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052273 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [67, 29, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 69, 96, 96, 96, 125, 125, 125, 125, 69, 69, 69, 69, 29, 29, 11, 1, 96, 125, 125, 125, 125, 125, 125, 125] 125 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: 463 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: REAL250005052273 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [27, 10, 27, 79, 116, 116, 116, 125, 125, 125, 125, 125, 10, 1, 10, 1, 1, 1, 1, 1, 27, 27, 27, 27, 79, 79, 116, 125, 10, 1, 1, 1, 1, 1, 1, 1] 125 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 444 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052273 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052273 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052273/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052273 Building REAL250005052274 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052274' /scratch/stefan/7921156/working/building/REAL250005052274 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052274 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052274/0 /scratch/stefan/7921156/working/building/REAL250005052274 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/404 `/scratch/stefan/7921156/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NN1C) `REAL250005052274.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052274 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 8, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [58, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 58, 81, 81, 81, 83, 83, 83, 83, 83, 58, 58, 58, 58, 21, 21, 9, 1, 81, 83, 83, 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: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052274 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 8, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 50, 79, 79, 79, 83, 83, 83, 83, 83, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 79, 83, 6, 1, 1, 2, 2, 2] 83 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052274 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052274 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052274/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052274 Building REAL250005052275 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052275' /scratch/stefan/7921156/working/building/REAL250005052275 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052275 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052275/0 /scratch/stefan/7921156/working/building/REAL250005052275 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/405 `/scratch/stefan/7921156/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052275.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052275 none CCC(OC)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 159, 111, 159, 165, 111, 111, 65, 18, 62, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 159, 165, 165, 165, 111, 65, 65, 65, 65, 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: 940 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052275 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052275 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052275/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052275 Building REAL250005052276 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052276' /scratch/stefan/7921156/working/building/REAL250005052276 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052276 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052276/0 /scratch/stefan/7921156/working/building/REAL250005052276 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/406 `/scratch/stefan/7921156/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052276.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052276 none COCCCCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 128, 110, 92, 29, 29, 29, 16, 12, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 198, 198, 128, 128, 128, 128, 92, 92, 29, 16, 16, 16, 16, 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: 1048 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052276 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052276 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052276/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052276 Building REAL250005052277 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052277' /scratch/stefan/7921156/working/building/REAL250005052277 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052277 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052277/0 /scratch/stefan/7921156/working/building/REAL250005052277 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/407 `/scratch/stefan/7921156/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052277.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052277 none CCCC(C)CC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 124, 181, 33, 33, 33, 29, 15, 29, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 183, 183, 183, 183, 124, 124, 33, 29, 29, 29, 29, 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: 913 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052277 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052277 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052277/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052277 Building REAL250005052278 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052278' /scratch/stefan/7921156/working/building/REAL250005052278 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052278 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052278/0 /scratch/stefan/7921156/working/building/REAL250005052278 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/408 `/scratch/stefan/7921156/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052278.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052278 none COC(C)CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 116, 140, 73, 73, 73, 47, 18, 47, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 140, 140, 116, 116, 73, 47, 47, 47, 47, 18, 18, 5, 1] 140 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052278 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052278 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052278/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052278 Building REAL250005052279 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052279' /scratch/stefan/7921156/working/building/REAL250005052279 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052279 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052279/0 /scratch/stefan/7921156/working/building/REAL250005052279 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/409 `/scratch/stefan/7921156/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052279.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052279 none C=CCCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 89, 89, 89, 66, 24, 66, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 181, 181, 89, 66, 66, 66, 66, 24, 24, 8, 1] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 877 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052279 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052279 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052279/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052279 Building REAL250005052280 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052280' /scratch/stefan/7921156/working/building/REAL250005052280 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052280 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052280/0 /scratch/stefan/7921156/working/building/REAL250005052280 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/410 `/scratch/stefan/7921156/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COCCC1) `REAL250005052280.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052280 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 72, 114, 114, 114, 201, 201, 201, 201, 201, 72, 72, 72, 72, 25, 25, 9, 1, 114, 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]) total number of confs: 543 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052280 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 47, 138, 196, 196, 196, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 138, 138, 196, 201, 12, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 749 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052280 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052280 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052280/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052280 Building REAL250005052281 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052281' /scratch/stefan/7921156/working/building/REAL250005052281 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052281 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052281/0 /scratch/stefan/7921156/working/building/REAL250005052281 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/411 `/scratch/stefan/7921156/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCOC1) `REAL250005052281.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052281 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 12, 5, 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, 7, 7, 3, 7, 3, 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, 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: [64, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 66, 105, 105, 105, 170, 170, 170, 170, 170, 66, 66, 66, 66, 28, 28, 9, 1, 105, 170, 170, 170, 170, 170, 170, 170, 170, 170] 170 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: 589 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052281 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 12, 5, 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, 7, 7, 3, 7, 3, 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, 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: [44, 11, 44, 115, 165, 165, 165, 170, 170, 170, 170, 170, 11, 1, 11, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 115, 115, 165, 170, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 170 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 626 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052281 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052281 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052281/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052281 Building REAL250005052282 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052282' /scratch/stefan/7921156/working/building/REAL250005052282 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052282 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052282/0 /scratch/stefan/7921156/working/building/REAL250005052282 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/412 `/scratch/stefan/7921156/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052282.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052282 none CCOCCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 171, 155, 77, 77, 77, 48, 16, 48, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 171, 171, 155, 155, 77, 48, 48, 48, 48, 16, 16, 4, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 764 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052282 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052282 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052282/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052282 Building REAL250005052283 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052283' /scratch/stefan/7921156/working/building/REAL250005052283 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052283 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052283/0 /scratch/stefan/7921156/working/building/REAL250005052283 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/413 `/scratch/stefan/7921156/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)NC(=O)C1=CSC=N1) `REAL250005052283.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052283 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSC=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.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [68, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 68, 91, 91, 91, 92, 92, 92, 92, 68, 68, 68, 68, 33, 33, 9, 1, 91, 92, 92] 92 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]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052283 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSC=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.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [15, 4, 15, 47, 86, 86, 86, 92, 92, 92, 92, 92, 4, 1, 4, 1, 1, 1, 1, 1, 15, 15, 15, 15, 47, 47, 86, 92, 4, 1, 1] 92 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 311 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052283 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052283 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052283/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052283 Building REAL250005052284 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052284' /scratch/stefan/7921156/working/building/REAL250005052284 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052284 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052284/0 /scratch/stefan/7921156/working/building/REAL250005052284 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/414 `/scratch/stefan/7921156/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052284.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052284 none COCC(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 123, 79, 123, 79, 79, 47, 20, 47, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 123, 123, 123, 123, 79, 47, 47, 47, 47, 20, 20, 7, 1] 151 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: 666 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052284 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052284 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052284/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052284 Building REAL250005052285 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052285' /scratch/stefan/7921156/working/building/REAL250005052285 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052285 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052285/0 /scratch/stefan/7921156/working/building/REAL250005052285 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/415 `/scratch/stefan/7921156/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052285.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052285 none C=CCOCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 125, 78, 43, 43, 43, 29, 8, 29, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 78, 78, 43, 29, 29, 29, 29, 8, 8, 2, 1] 201 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 798 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052285 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052285 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052285/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052285 Building REAL250005052286 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052286' /scratch/stefan/7921156/working/building/REAL250005052286 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052286 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052286/0 /scratch/stefan/7921156/working/building/REAL250005052286 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/416 `/scratch/stefan/7921156/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)NC(=O)C1=COC=N1) `REAL250005052286.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052286 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [73, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 73, 89, 89, 89, 90, 90, 90, 90, 73, 73, 73, 73, 33, 33, 9, 1, 89, 90, 90] 90 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]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052286 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [16, 4, 16, 47, 85, 85, 85, 90, 90, 90, 90, 90, 4, 1, 4, 1, 1, 1, 1, 1, 16, 16, 16, 16, 47, 47, 85, 90, 4, 1, 1] 90 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 311 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052286 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052286 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052286/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052286 Building REAL250005052287 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052287' /scratch/stefan/7921156/working/building/REAL250005052287 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052287 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052287/0 /scratch/stefan/7921156/working/building/REAL250005052287 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/417 `/scratch/stefan/7921156/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCC(=O)N1) `REAL250005052287.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052287 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [64, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 66, 97, 97, 97, 141, 141, 141, 141, 141, 141, 66, 66, 66, 66, 28, 28, 10, 1, 97, 141, 141, 141, 141, 141] 141 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: 506 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: REAL250005052287 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [37, 11, 37, 92, 133, 133, 133, 141, 141, 141, 141, 141, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 92, 92, 133, 141, 11, 1, 1, 1, 1, 1] 141 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 519 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052287 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052287 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052287/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052287 Building REAL250005052288 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052288' /scratch/stefan/7921156/working/building/REAL250005052288 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052288 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052288/0 /scratch/stefan/7921156/working/building/REAL250005052288 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/418 `/scratch/stefan/7921156/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005052288.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052288 none CC1=NC=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 50, 76, 76, 76, 78, 78, 78, 78, 78, 1, 2, 2, 2, 1, 6, 22, 22, 22, 22, 50, 50, 76, 78, 1] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 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: REAL250005052288 none CC1=NC=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 67, 67, 67, 48, 18, 47, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 67, 48, 48, 48, 48, 18, 18, 8, 1, 78] 78 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052288 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052288 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052288/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052288 Building REAL250005052289 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052289' /scratch/stefan/7921156/working/building/REAL250005052289 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005052289 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052289/0 /scratch/stefan/7921156/working/building/REAL250005052289 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/419 `/scratch/stefan/7921156/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)NC(=O)C1CCC[N@@H+]1C) `REAL250005052289.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052289 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC[N@@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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 7 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: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052289 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC[N@@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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 6, 6, 6, 6, 7, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 7, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 7 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052289 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052289/1 /scratch/stefan/7921156/working/building/REAL250005052289 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/420 `/scratch/stefan/7921156/working/3D/420' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC[N@H+]1C) `REAL250005052289.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052289/1/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: REAL250005052289 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC[N@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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 7 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: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052289 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC[N@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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 6, 6, 6, 6, 7, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 7, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 7 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052289 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `2' /scratch/stefan/7921156/working/building/REAL250005052289/2 /scratch/stefan/7921156/working/building/REAL250005052289 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 2 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/421 `/scratch/stefan/7921156/working/3D/421' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCN1C) `REAL250005052289.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005052289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052289/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052289 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 1, 11, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [77, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 79, 115, 115, 115, 120, 120, 120, 120, 120, 79, 79, 79, 79, 30, 30, 9, 1, 115, 120, 120, 120, 120, 120, 120, 120, 120, 120, 120] 120 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: 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: REAL250005052289 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 1, 11, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 20, 67, 115, 115, 115, 120, 120, 120, 120, 120, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 67, 67, 115, 120, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 120 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39]) total number of confs: 420 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052289 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052289 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052289/0.* 2: /scratch/stefan/7921156/working/building/REAL250005052289/2.* 1: /scratch/stefan/7921156/working/building/REAL250005052289/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052289 Building REAL250005052290 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052290' /scratch/stefan/7921156/working/building/REAL250005052290 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052290 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052290/0 /scratch/stefan/7921156/working/building/REAL250005052290 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/422 `/scratch/stefan/7921156/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052290.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052290 none CCC(=O)NCC(=O)NC(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 102, 71, 71, 71, 38, 13, 38, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 154, 102, 102, 71, 38, 38, 38, 38, 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: 872 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052290 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052290 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052290/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052290 Building REAL250005052291 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052291' /scratch/stefan/7921156/working/building/REAL250005052291 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052291 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052291/0 /scratch/stefan/7921156/working/building/REAL250005052291 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/423 `/scratch/stefan/7921156/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CC(C)(C)C) `REAL250005052291.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052291 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 26, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 78, 120, 120, 120, 196, 196, 201, 201, 201, 78, 78, 78, 78, 26, 26, 9, 1, 120, 196, 196, 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: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052291 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052291 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052291/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052291 Building REAL250005052292 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052292' /scratch/stefan/7921156/working/building/REAL250005052292 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052292 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052292/0 /scratch/stefan/7921156/working/building/REAL250005052292 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/424 `/scratch/stefan/7921156/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052292.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052292 none CC(C#N)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 75, 119, 119, 75, 75, 53, 24, 51, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 75, 53, 53, 53, 53, 24, 24, 9, 1] 119 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: 505 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052292 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052292 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052292/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052292 Building REAL250005052293 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052293' /scratch/stefan/7921156/working/building/REAL250005052293 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052293 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052293/0 /scratch/stefan/7921156/working/building/REAL250005052293 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/425 `/scratch/stefan/7921156/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052293.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052293 none CCCC(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 166, 73, 166, 73, 73, 59, 21, 58, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 197, 193, 193, 166, 166, 166, 166, 73, 59, 59, 59, 59, 21, 21, 4, 1] 201 rigid atoms, others: [39, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 920 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052293 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052293 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052293/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052293 Building REAL250005052294 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052294' /scratch/stefan/7921156/working/building/REAL250005052294 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052294 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052294/0 /scratch/stefan/7921156/working/building/REAL250005052294 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/426 `/scratch/stefan/7921156/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(=O)C(C)(C)C) `REAL250005052294.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052294 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)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.2', 'O.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 11, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 25, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 71, 124, 124, 124, 190, 190, 201, 201, 201, 71, 71, 71, 71, 25, 25, 8, 1, 124, 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]) total number of confs: 731 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052294 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052294 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052294/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052294 Building REAL250005052295 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052295' /scratch/stefan/7921156/working/building/REAL250005052295 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052295 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052295/0 /scratch/stefan/7921156/working/building/REAL250005052295 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/427 `/scratch/stefan/7921156/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC1CC1) `REAL250005052295.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052295 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 144, 156, 201, 201, 30, 30, 30, 30, 11, 11, 4, 1, 50, 144, 144, 162, 162, 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: 867 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052295 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 32, 76, 149, 201, 201, 201, 201, 201, 201, 201, 201, 32, 7, 32, 3, 1, 1, 1, 1, 76, 76, 76, 76, 149, 149, 201, 201, 32, 7, 7, 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: 819 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052295 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052295 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052295/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052295 Building REAL250005052296 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052296' /scratch/stefan/7921156/working/building/REAL250005052296 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052296 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052296/0 /scratch/stefan/7921156/working/building/REAL250005052296 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/428 `/scratch/stefan/7921156/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052296.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052296 none CCCCOCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 118, 89, 29, 29, 29, 16, 10, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 140, 140, 89, 89, 29, 16, 16, 16, 16, 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: 852 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052296 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052296 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052296/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052296 Building REAL250005052297 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052297' /scratch/stefan/7921156/working/building/REAL250005052297 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052297 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052297/0 /scratch/stefan/7921156/working/building/REAL250005052297 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/429 `/scratch/stefan/7921156/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=NOC=C1) `REAL250005052297.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052297 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 12, 1, 1, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 46, 79, 79, 79, 162, 201, 201, 201, 201, 46, 46, 46, 46, 20, 20, 7, 1, 79, 162, 162, 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: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052297 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 12, 1, 1, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 30, 74, 148, 198, 198, 198, 201, 201, 201, 201, 201, 30, 5, 30, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 148, 148, 198, 201, 30, 5, 5, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 798 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052297 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052297 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052297/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052297 Building REAL250005052298 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052298' /scratch/stefan/7921156/working/building/REAL250005052298 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052298 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052298/0 /scratch/stefan/7921156/working/building/REAL250005052298 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/430 `/scratch/stefan/7921156/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CCOC1) `REAL250005052298.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052298 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 12, 5, 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, 7, 7, 3, 7, 3, 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, 7] 0 hydrogens 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, 18, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 45, 73, 73, 73, 177, 201, 201, 201, 201, 45, 45, 45, 45, 18, 18, 5, 1, 73, 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]) total number of confs: 807 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: REAL250005052298 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 12, 5, 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, 7, 7, 3, 7, 3, 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, 7] 0 hydrogens 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, 35, 85, 155, 200, 200, 200, 201, 201, 201, 201, 201, 35, 6, 35, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 155, 155, 200, 201, 35, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 793 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052298 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052298 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052298/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052298 Building REAL250005052299 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052299' /scratch/stefan/7921156/working/building/REAL250005052299 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052299 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052299/0 /scratch/stefan/7921156/working/building/REAL250005052299 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/431 `/scratch/stefan/7921156/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)NC(=O)C1CC=CC1) `REAL250005052299.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052299 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [75, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 77, 114, 114, 114, 201, 201, 201, 201, 77, 77, 77, 77, 31, 31, 9, 1, 114, 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]) total number of confs: 703 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052299 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [40, 9, 40, 120, 190, 190, 190, 201, 201, 201, 201, 201, 9, 1, 9, 1, 1, 1, 1, 1, 40, 40, 40, 40, 120, 120, 190, 201, 9, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 719 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052299 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052299 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052299/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052299 Building REAL250005052300 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052300' /scratch/stefan/7921156/working/building/REAL250005052300 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052300 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052300/0 /scratch/stefan/7921156/working/building/REAL250005052300 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/432 `/scratch/stefan/7921156/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=NNC=C1) `REAL250005052300.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052300 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [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] 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: [51, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 51, 72, 72, 72, 154, 185, 185, 185, 185, 51, 51, 51, 51, 21, 21, 8, 1, 72, 154, 154, 185, 185, 185] 185 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: 668 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052300 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [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] 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: [82, 46, 82, 143, 182, 182, 182, 185, 185, 185, 185, 185, 46, 9, 46, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 143, 143, 182, 185, 46, 9, 9, 1, 1, 1] 185 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 725 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052300 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052300 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052300/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052300 Building REAL250005052301 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052301' /scratch/stefan/7921156/working/building/REAL250005052301 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052301 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052301/0 /scratch/stefan/7921156/working/building/REAL250005052301 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/433 `/scratch/stefan/7921156/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)NC(=O)CC1CCC1) `REAL250005052301.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052301 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 60, 96, 96, 96, 171, 201, 201, 201, 60, 60, 60, 60, 20, 20, 4, 1, 96, 171, 171, 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: 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: REAL250005052301 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 38, 96, 161, 201, 201, 201, 201, 201, 201, 201, 201, 38, 6, 38, 1, 1, 1, 1, 1, 96, 96, 96, 96, 161, 161, 201, 201, 38, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 793 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052301 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052301 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052301/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052301 Building REAL250005052302 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052302' /scratch/stefan/7921156/working/building/REAL250005052302 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052302 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052302/0 /scratch/stefan/7921156/working/building/REAL250005052302 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/434 `/scratch/stefan/7921156/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)OC=N1) `REAL250005052302.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052302 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 33, 33, 93, 149, 149, 149, 155, 155, 155, 155, 155, 1, 1, 1, 2, 2, 2, 9, 33, 33, 33, 33, 93, 93, 149, 155, 1] 155 rigid atoms, others: [0, 1, 2, 3, 33, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 564 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: REAL250005052302 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 123, 123, 123, 87, 32, 85, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 155, 123, 87, 87, 87, 87, 32, 32, 9, 1, 155] 155 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 515 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052302 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052302 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052302/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052302 Building REAL250005052303 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052303' /scratch/stefan/7921156/working/building/REAL250005052303 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052303 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052303/0 /scratch/stefan/7921156/working/building/REAL250005052303 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/435 `/scratch/stefan/7921156/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)NC(=O)C(C)C1CC1) `REAL250005052303.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052303 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 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 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [84, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 86, 120, 120, 120, 197, 197, 198, 198, 86, 86, 86, 86, 37, 37, 11, 1, 120, 197, 197, 197, 197, 198, 198, 198, 198, 198] 198 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: 840 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052303 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 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 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [58, 20, 58, 130, 185, 185, 185, 198, 198, 198, 198, 198, 20, 4, 20, 1, 4, 1, 1, 1, 58, 58, 58, 58, 130, 130, 185, 198, 20, 4, 4, 4, 4, 1, 1, 1, 1, 1] 198 rigid atoms, others: [33, 34, 35, 36, 37, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 716 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052303 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052303 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052303/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052303 Building REAL250005052304 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052304' /scratch/stefan/7921156/working/building/REAL250005052304 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052304 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052304/0 /scratch/stefan/7921156/working/building/REAL250005052304 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/436 `/scratch/stefan/7921156/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)NC(=O)C1C2CCCC21) `REAL250005052304.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052304 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1C2CCCC21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [62, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 64, 96, 96, 96, 111, 111, 111, 111, 111, 64, 64, 64, 64, 28, 28, 8, 1, 96, 111, 111, 111, 111, 111, 111, 111, 111, 111] 111 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: 426 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: REAL250005052304 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1C2CCCC21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [13, 3, 13, 54, 105, 105, 105, 111, 111, 111, 111, 111, 3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 54, 54, 105, 111, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 111 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 378 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052304 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052304 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052304/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052304 Building REAL250005052305 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052305' /scratch/stefan/7921156/working/building/REAL250005052305 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052305 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052305/0 /scratch/stefan/7921156/working/building/REAL250005052305 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/437 `/scratch/stefan/7921156/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC1CCC1) `REAL250005052305.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052305 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 35, 43, 43, 43, 133, 148, 201, 201, 201, 35, 35, 35, 35, 16, 16, 4, 1, 43, 133, 133, 171, 171, 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: 944 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052305 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 54, 102, 167, 201, 201, 201, 201, 201, 201, 201, 201, 54, 13, 54, 6, 1, 1, 1, 1, 1, 102, 102, 102, 102, 167, 167, 201, 201, 54, 13, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 833 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052305 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052305 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052305/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052305 Building REAL250005052306 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052306' /scratch/stefan/7921156/working/building/REAL250005052306 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052306 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052306/0 /scratch/stefan/7921156/working/building/REAL250005052306 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/438 `/scratch/stefan/7921156/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C=CN1) `REAL250005052306.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052306 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 12, 12, 12, 38, 38, 117, 182, 182, 182, 191, 191, 191, 191, 191, 1, 1, 1, 2, 2, 2, 12, 38, 38, 38, 38, 117, 117, 182, 191, 1, 1, 1] 191 rigid atoms, others: [0, 1, 2, 3, 35, 33, 34, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 681 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: REAL250005052306 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 120, 120, 120, 78, 31, 77, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 191, 191, 191, 191, 191, 191, 120, 78, 78, 78, 78, 31, 31, 9, 1, 191, 191, 191] 191 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 558 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052306 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052306 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052306/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052306 Building REAL250005052307 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052307' /scratch/stefan/7921156/working/building/REAL250005052307 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052307 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052307/0 /scratch/stefan/7921156/working/building/REAL250005052307 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/439 `/scratch/stefan/7921156/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052307.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052307 none CC=C(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 118, 177, 118, 118, 78, 32, 76, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 177, 177, 118, 78, 78, 78, 78, 32, 32, 9, 1] 177 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: 663 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052307 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052307 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052307/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052307 Building REAL250005052308 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052308' /scratch/stefan/7921156/working/building/REAL250005052308 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052308 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052308/0 /scratch/stefan/7921156/working/building/REAL250005052308 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/440 `/scratch/stefan/7921156/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)C1) `REAL250005052308.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052308 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 81, 124, 124, 124, 201, 201, 201, 201, 81, 81, 81, 81, 31, 31, 9, 1, 124, 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]) total number of confs: 708 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: REAL250005052308 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 12, 43, 125, 189, 189, 189, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 43, 43, 43, 43, 125, 125, 189, 201, 12, 1, 1, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 36, 37, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 727 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052308 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052308 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052308/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052308 Building REAL250005052309 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052309' /scratch/stefan/7921156/working/building/REAL250005052309 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052309 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052309/0 /scratch/stefan/7921156/working/building/REAL250005052309 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/441 `/scratch/stefan/7921156/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=C1CCC1) `REAL250005052309.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052309 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [73, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 76, 121, 121, 121, 188, 188, 188, 188, 76, 76, 76, 76, 26, 26, 9, 1, 121, 188, 188, 188, 188, 188, 188, 188] 188 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: 678 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: REAL250005052309 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [48, 11, 48, 129, 180, 180, 180, 188, 188, 188, 188, 188, 11, 1, 11, 1, 1, 1, 1, 1, 48, 48, 48, 48, 129, 129, 180, 188, 11, 1, 1, 1, 1, 1, 1, 1] 188 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 692 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052309 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052309 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052309/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052309 Building REAL250005052310 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052310' /scratch/stefan/7921156/working/building/REAL250005052310 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052310 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052310/0 /scratch/stefan/7921156/working/building/REAL250005052310 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/442 `/scratch/stefan/7921156/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)CC) `REAL250005052310.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052310 none CCC(=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 106, 106, 68, 68, 68, 52, 19, 52, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 106, 146, 149, 149, 149, 149, 149, 106, 68, 52, 52, 52, 52, 19, 19, 4, 1, 146, 146, 146, 146, 146] 201 rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 896 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052310 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052310 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052310/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052310 Building REAL250005052311 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052311' /scratch/stefan/7921156/working/building/REAL250005052311 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052311 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052311/0 /scratch/stefan/7921156/working/building/REAL250005052311 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/443 `/scratch/stefan/7921156/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052311.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052311 none CC(C)=C(F)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 102, 132, 102, 102, 69, 26, 67, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 132, 132, 102, 69, 69, 69, 69, 26, 26, 9, 1] 132 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 498 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052311 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052311 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052311/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052311 Building REAL250005052312 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052312' /scratch/stefan/7921156/working/building/REAL250005052312 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052312 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052312/0 /scratch/stefan/7921156/working/building/REAL250005052312 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/444 `/scratch/stefan/7921156/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCC1) `REAL250005052312.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052312 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [65, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 65, 89, 89, 89, 91, 91, 91, 91, 65, 65, 65, 65, 27, 27, 9, 1, 89, 91, 91, 91, 91, 91, 91, 91] 91 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: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052312 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 27, 63, 85, 85, 85, 91, 91, 91, 91, 91, 9, 1, 9, 1, 1, 1, 1, 1, 27, 27, 27, 27, 63, 63, 85, 91, 9, 1, 1, 1, 1, 1, 1, 1] 91 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 345 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052312 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052312 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052312/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052312 Building REAL250005052313 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052313' /scratch/stefan/7921156/working/building/REAL250005052313 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052313 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052313/0 /scratch/stefan/7921156/working/building/REAL250005052313 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/445 `/scratch/stefan/7921156/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN(C)C=C1) `REAL250005052313.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052313 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN(C)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.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 5, 1, 1, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [86, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 88, 126, 126, 126, 174, 174, 174, 174, 174, 88, 88, 88, 88, 32, 32, 10, 1, 126, 174, 174, 174, 174, 174, 174] 174 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: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052313 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN(C)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.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 5, 1, 1, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 23, 91, 163, 163, 163, 174, 174, 174, 174, 174, 5, 1, 5, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 91, 91, 163, 174, 5, 1, 2, 2, 2, 1, 1] 174 rigid atoms, others: [34, 35, 13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 607 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052313 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052313 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052313/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052313 Building REAL250005052314 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052314' /scratch/stefan/7921156/working/building/REAL250005052314 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052314 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052314/0 /scratch/stefan/7921156/working/building/REAL250005052314 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/446 `/scratch/stefan/7921156/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN(C)C=N1) `REAL250005052314.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052314 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN(C)C=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.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 5, 1, 8, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [65, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 66, 89, 89, 89, 90, 90, 90, 90, 90, 66, 66, 66, 66, 32, 32, 9, 1, 89, 90, 90, 90, 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]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052314 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN(C)C=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.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 5, 1, 8, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 45, 81, 81, 81, 90, 90, 90, 90, 90, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 45, 45, 81, 90, 6, 1, 2, 2, 2, 1] 90 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 316 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052314 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052314 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052314/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052314 Building REAL250005052315 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052315' /scratch/stefan/7921156/working/building/REAL250005052315 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052315 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052315/0 /scratch/stefan/7921156/working/building/REAL250005052315 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/447 `/scratch/stefan/7921156/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCCO1) `REAL250005052315.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052315 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 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, 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: [86, 41, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 86, 125, 125, 125, 162, 162, 162, 162, 162, 86, 86, 86, 86, 41, 41, 11, 1, 125, 162, 162, 162, 162, 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, 37, 38]) total number of confs: 584 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052315 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 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, 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: [37, 11, 37, 104, 154, 154, 154, 162, 162, 162, 162, 162, 11, 1, 11, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 104, 104, 154, 162, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 162 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 582 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052315 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052315 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052315/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052315 Building REAL250005052316 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052316' /scratch/stefan/7921156/working/building/REAL250005052316 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052316 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052316/0 /scratch/stefan/7921156/working/building/REAL250005052316 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/448 `/scratch/stefan/7921156/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1(C)C) `REAL250005052316.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052316 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [74, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 75, 115, 115, 115, 157, 157, 157, 157, 75, 75, 75, 75, 31, 31, 11, 1, 115, 157, 157, 157, 157, 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, 36, 37]) total number of confs: 574 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052316 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [33, 10, 33, 95, 148, 148, 148, 157, 157, 157, 157, 157, 10, 1, 10, 1, 1, 1, 1, 1, 33, 33, 33, 33, 95, 95, 148, 157, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2] 157 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 571 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052316 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052316 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052316/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052316 Building REAL250005052317 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052317' /scratch/stefan/7921156/working/building/REAL250005052317 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052317 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052317/0 /scratch/stefan/7921156/working/building/REAL250005052317 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/449 `/scratch/stefan/7921156/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052317.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052317 none CCC(C)OCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 173, 149, 173, 114, 69, 69, 69, 42, 12, 41, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 173, 173, 173, 173, 114, 114, 69, 42, 42, 42, 42, 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: 848 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052317 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052317 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052317/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052317 Building REAL250005052318 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052318' /scratch/stefan/7921156/working/building/REAL250005052318 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052318 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052318/0 /scratch/stefan/7921156/working/building/REAL250005052318 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/450 `/scratch/stefan/7921156/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CC1(C)C) `REAL250005052318.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052318 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [76, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 77, 118, 118, 118, 159, 159, 159, 159, 159, 77, 77, 77, 77, 31, 31, 10, 1, 118, 159, 159, 159, 159, 159, 159, 159, 159] 159 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: 580 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052318 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [33, 10, 33, 96, 149, 149, 149, 159, 159, 159, 159, 159, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 96, 96, 149, 159, 10, 1, 1, 1, 1, 1, 2, 2, 2] 159 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 571 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052318 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052318 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052318/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052318 Building REAL250005052319 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052319' /scratch/stefan/7921156/working/building/REAL250005052319 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052319 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052319/0 /scratch/stefan/7921156/working/building/REAL250005052319 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/451 `/scratch/stefan/7921156/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCCO1) `REAL250005052319.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052319 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [65, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 66, 99, 99, 99, 116, 116, 116, 116, 116, 66, 66, 66, 66, 25, 25, 7, 1, 99, 116, 116, 116, 116, 116, 116] 116 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: 427 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: REAL250005052319 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [31, 9, 31, 78, 114, 114, 114, 116, 116, 116, 116, 116, 9, 1, 9, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 78, 78, 114, 116, 9, 1, 1, 1, 1, 1, 1] 116 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 428 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052319 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052319 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052319/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052319 Building REAL250005052320 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052320' /scratch/stefan/7921156/working/building/REAL250005052320 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052320 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052320/0 /scratch/stefan/7921156/working/building/REAL250005052320 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/452 `/scratch/stefan/7921156/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052320.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052320 none C#CCCCCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 137, 129, 111, 41, 41, 41, 27, 11, 27, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 201, 201, 138, 138, 134, 134, 111, 111, 41, 27, 27, 27, 27, 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: 947 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052320 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052320 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052320/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052320 Building REAL250005052321 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052321' /scratch/stefan/7921156/working/building/REAL250005052321 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052321 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052321/0 /scratch/stefan/7921156/working/building/REAL250005052321 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/453 `/scratch/stefan/7921156/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COC(C)(C)C) `REAL250005052321.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052321 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COC(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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 31, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 92, 156, 156, 156, 201, 201, 201, 201, 201, 92, 92, 92, 92, 31, 31, 8, 1, 156, 201, 201, 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: 830 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052321 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052321 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052321/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052321 Building REAL250005052322 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052322' /scratch/stefan/7921156/working/building/REAL250005052322 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052322 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052322/0 /scratch/stefan/7921156/working/building/REAL250005052322 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/454 `/scratch/stefan/7921156/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052322.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052322 none CCNC(=O)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 111, 151, 62, 62, 62, 42, 19, 42, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 151, 111, 111, 62, 42, 42, 42, 42, 19, 19, 6, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 913 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052322 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052322 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052322/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052322 Building REAL250005052323 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052323' /scratch/stefan/7921156/working/building/REAL250005052323 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052323 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052323/0 /scratch/stefan/7921156/working/building/REAL250005052323 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/455 `/scratch/stefan/7921156/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052323.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052323 none COC(C)CCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 92, 128, 95, 42, 42, 42, 30, 15, 30, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 128, 128, 128, 124, 128, 128, 128, 109, 109, 95, 95, 42, 30, 30, 30, 30, 15, 15, 4, 1] 128 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 653 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052323 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052323 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052323/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052323 Building REAL250005052324 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052324' /scratch/stefan/7921156/working/building/REAL250005052324 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052324 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052324/0 /scratch/stefan/7921156/working/building/REAL250005052324 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/456 `/scratch/stefan/7921156/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CN=C1) `REAL250005052324.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052324 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CN=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.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 3, 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: [76, 26, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 77, 100, 100, 100, 101, 101, 100, 101, 101, 77, 77, 77, 77, 26, 26, 10, 1, 100, 101, 100, 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]) total number of confs: 385 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: REAL250005052324 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CN=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.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 3, 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: [16, 5, 16, 47, 75, 75, 75, 82, 82, 82, 82, 82, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 47, 47, 75, 82, 5, 1, 1, 1] 82 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052324 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052324 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052324/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052324 Building REAL250005052325 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052325' /scratch/stefan/7921156/working/building/REAL250005052325 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052325 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052325/0 /scratch/stefan/7921156/working/building/REAL250005052325 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/457 `/scratch/stefan/7921156/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCOCC1) `REAL250005052325.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052325 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', '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, 1, 11, 1, 1, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [71, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 72, 102, 102, 102, 149, 149, 149, 149, 149, 72, 72, 72, 72, 31, 31, 11, 1, 102, 149, 149, 149, 149, 149, 149, 149] 149 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: 471 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052325 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', '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, 1, 11, 1, 1, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [45, 11, 45, 103, 140, 140, 140, 149, 149, 149, 149, 149, 11, 1, 11, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 103, 103, 140, 149, 11, 1, 1, 1, 1, 1, 1, 1] 149 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 547 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052325 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052325 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052325/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052325 Building REAL250005052326 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052326' /scratch/stefan/7921156/working/building/REAL250005052326 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052326 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052326/0 /scratch/stefan/7921156/working/building/REAL250005052326 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/458 `/scratch/stefan/7921156/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=COC=C1) `REAL250005052326.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052326 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 12, 1, 1, 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, 7, 3, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 40, 67, 67, 67, 106, 201, 201, 201, 201, 40, 40, 40, 40, 17, 17, 5, 1, 67, 106, 106, 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: 598 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052326 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 12, 1, 1, 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, 7, 3, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 16, 55, 139, 200, 200, 200, 201, 201, 201, 201, 201, 16, 4, 16, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 139, 139, 200, 201, 16, 4, 4, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 788 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052326 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052326 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052326/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052326 Building REAL250005052327 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052327' /scratch/stefan/7921156/working/building/REAL250005052327 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052327 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052327/0 /scratch/stefan/7921156/working/building/REAL250005052327 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/459 `/scratch/stefan/7921156/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=CO1) `REAL250005052327.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052327 none CC1=NC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 6, 17, 17, 54, 96, 96, 96, 101, 101, 101, 101, 101, 1, 1, 2, 2, 2, 6, 17, 17, 17, 17, 54, 54, 96, 101, 1] 101 rigid atoms, others: [0, 1, 2, 3, 4, 33, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052327 none CC1=NC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 99, 99, 99, 69, 34, 69, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 99, 69, 69, 69, 69, 34, 34, 9, 1, 101] 101 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 371 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052327 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052327 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052327/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052327 Building REAL250005052328 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052328' /scratch/stefan/7921156/working/building/REAL250005052328 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052328 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052328/0 /scratch/stefan/7921156/working/building/REAL250005052328 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/460 `/scratch/stefan/7921156/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)NC(N)=O) `REAL250005052328.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052328 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)NC(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.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [80, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 80, 119, 119, 119, 178, 178, 178, 187, 187, 187, 80, 80, 80, 80, 35, 35, 11, 1, 119, 178, 178, 178, 187, 187, 187] 187 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]) total number of confs: 774 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052328 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052328 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052328/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052328 Building REAL250005052329 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052329' /scratch/stefan/7921156/working/building/REAL250005052329 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052329 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052329/0 /scratch/stefan/7921156/working/building/REAL250005052329 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/461 `/scratch/stefan/7921156/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=CO1) `REAL250005052329.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052329 none CC1=CC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 23, 23, 88, 148, 148, 148, 158, 158, 158, 158, 158, 1, 1, 2, 2, 2, 1, 5, 23, 23, 23, 23, 88, 88, 148, 158, 1] 158 rigid atoms, others: [0, 1, 2, 3, 4, 34, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 562 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052329 none CC1=CC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 120, 120, 120, 83, 31, 82, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 158, 158, 120, 83, 83, 83, 83, 31, 31, 11, 1, 158] 158 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34]) total number of confs: 528 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052329 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052329 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052329/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052329 Building REAL250005052330 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052330' /scratch/stefan/7921156/working/building/REAL250005052330 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052330 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052330/0 /scratch/stefan/7921156/working/building/REAL250005052330 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/462 `/scratch/stefan/7921156/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052330.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052330 none CCC(C)CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 145, 182, 47, 47, 47, 37, 17, 37, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 183, 183, 183, 183, 145, 145, 47, 37, 37, 37, 37, 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: 887 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052330 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052330 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052330/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052330 Building REAL250005052331 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052331' /scratch/stefan/7921156/working/building/REAL250005052331 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052331 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052331/0 /scratch/stefan/7921156/working/building/REAL250005052331 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/463 `/scratch/stefan/7921156/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052331.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052331 none C#CCCCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 137, 123, 34, 34, 34, 22, 10, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 194, 188, 156, 156, 123, 123, 34, 22, 22, 22, 22, 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: 972 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052331 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052331 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052331/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052331 Building REAL250005052332 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052332' /scratch/stefan/7921156/working/building/REAL250005052332 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052332 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052332/0 /scratch/stefan/7921156/working/building/REAL250005052332 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/464 `/scratch/stefan/7921156/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052332.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052332 none C=CC(C)(O)CC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 48, 64, 64, 33, 33, 33, 22, 9, 22, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64, 192, 48, 48, 33, 22, 22, 22, 22, 9, 9, 3, 1] 192 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 487 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052332 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052332 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052332/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052332 Building REAL250005052333 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052333' /scratch/stefan/7921156/working/building/REAL250005052333 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052333 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052333/0 /scratch/stefan/7921156/working/building/REAL250005052333 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/465 `/scratch/stefan/7921156/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(C)(C)O) `REAL250005052333.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052333 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 564 conformations in input total number of sets (complete confs): 564 using faster count positions algorithm for large data unique positions, atoms: [64, 25, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 65, 100, 100, 100, 162, 185, 187, 188, 65, 65, 65, 65, 25, 25, 9, 1, 100, 162, 162, 188, 188, 188, 188, 188, 188, 564] 564 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: 1389 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052333 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052333 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052333/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052333 Building REAL250005052334 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052334' /scratch/stefan/7921156/working/building/REAL250005052334 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052334 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052334/0 /scratch/stefan/7921156/working/building/REAL250005052334 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/466 `/scratch/stefan/7921156/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005052334.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052334 none COC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 153, 97, 97, 97, 60, 17, 58, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 153, 201, 201, 159, 159, 159, 153, 97, 60, 60, 60, 60, 17, 17, 4, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 859 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: REAL250005052334 none COC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 7, 24, 24, 24, 63, 63, 138, 200, 200, 200, 201, 201, 201, 201, 201, 1, 1, 1, 15, 15, 15, 7, 24, 63, 63, 63, 63, 138, 138, 200, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 2, 18, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 784 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052334 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052334 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052334/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052334 Building REAL250005052335 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052335' /scratch/stefan/7921156/working/building/REAL250005052335 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052335 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052335/0 /scratch/stefan/7921156/working/building/REAL250005052335 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/467 `/scratch/stefan/7921156/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)NC=C1) `REAL250005052335.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052335 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 12, 12, 11, 40, 40, 113, 167, 167, 167, 171, 171, 171, 171, 171, 1, 1, 1, 2, 2, 2, 12, 40, 40, 40, 40, 113, 113, 167, 171, 1, 1, 1] 171 rigid atoms, others: [0, 1, 2, 3, 35, 33, 34, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 637 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: REAL250005052335 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 101, 101, 101, 68, 26, 66, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 171, 171, 101, 68, 68, 68, 68, 26, 26, 9, 1, 171, 171, 171] 171 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 489 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052335 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052335 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052335/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052335 Building REAL250005052336 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052336' /scratch/stefan/7921156/working/building/REAL250005052336 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052336 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052336/0 /scratch/stefan/7921156/working/building/REAL250005052336 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/468 `/scratch/stefan/7921156/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=NN1C) `REAL250005052336.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052336 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 8, 8, 5, 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, 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] 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: [55, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 55, 78, 78, 78, 82, 82, 82, 82, 82, 55, 55, 55, 55, 24, 24, 9, 1, 78, 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]) total number of confs: 290 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: REAL250005052336 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 8, 8, 5, 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, 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] 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: [16, 6, 16, 51, 78, 78, 78, 82, 82, 82, 82, 82, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 51, 51, 78, 82, 6, 1, 2, 2, 2] 82 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 297 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052336 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052336 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052336/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052336 Building REAL250005052337 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052337' /scratch/stefan/7921156/working/building/REAL250005052337 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052337 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052337/0 /scratch/stefan/7921156/working/building/REAL250005052337 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/469 `/scratch/stefan/7921156/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=O)N1) `REAL250005052337.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052337 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [50, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 52, 69, 69, 69, 84, 84, 84, 84, 84, 52, 52, 52, 52, 23, 23, 9, 1, 69, 84, 84, 84, 84] 84 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: 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: REAL250005052337 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [24, 10, 24, 54, 80, 80, 80, 84, 84, 84, 84, 84, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 54, 54, 80, 84, 10, 1, 1, 1, 1] 84 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 307 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052337 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052337 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052337/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052337 Building REAL250005052338 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052338' /scratch/stefan/7921156/working/building/REAL250005052338 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052338 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052338/0 /scratch/stefan/7921156/working/building/REAL250005052338 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/470 `/scratch/stefan/7921156/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052338.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052338 none CCCCC(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 180, 129, 48, 129, 48, 48, 40, 15, 40, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 192, 184, 184, 129, 129, 129, 129, 48, 40, 40, 40, 40, 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: 935 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052338 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052338 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052338/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052338 Building REAL250005052339 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052339' /scratch/stefan/7921156/working/building/REAL250005052339 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052339 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052339/0 /scratch/stefan/7921156/working/building/REAL250005052339 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/471 `/scratch/stefan/7921156/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(C)C1) `REAL250005052339.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052339 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 71, 113, 113, 113, 201, 201, 201, 201, 201, 71, 71, 71, 71, 25, 25, 8, 1, 113, 201, 201, 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: 689 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: REAL250005052339 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 12, 45, 135, 196, 196, 196, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 135, 135, 196, 201, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 39, 40, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 738 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052339 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052339 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052339/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052339 Building REAL250005052340 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052340' /scratch/stefan/7921156/working/building/REAL250005052340 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052340 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052340/0 /scratch/stefan/7921156/working/building/REAL250005052340 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/472 `/scratch/stefan/7921156/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052340.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052340 none CC(C)[C@@H](O)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 185, 201, 129, 185, 185, 129, 129, 72, 24, 70, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 555, 129, 72, 72, 72, 72, 24, 24, 8, 1] 603 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1381 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052340 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052340 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052340/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052340 Building REAL250005052341 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052341' /scratch/stefan/7921156/working/building/REAL250005052341 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052341 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052341/0 /scratch/stefan/7921156/working/building/REAL250005052341 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/473 `/scratch/stefan/7921156/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN(C)N=N1) `REAL250005052341.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052341 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN(C)N=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.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 5, 8, 8, 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, 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] 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: [66, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 67, 83, 83, 83, 87, 87, 87, 87, 87, 67, 67, 67, 67, 22, 22, 7, 1, 83, 87, 87, 87, 87] 87 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: 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: REAL250005052341 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN(C)N=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.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 5, 8, 8, 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, 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] 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: [20, 6, 20, 57, 84, 84, 84, 87, 87, 87, 87, 87, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 57, 57, 84, 87, 6, 1, 2, 2, 2] 87 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052341 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052341 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052341/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052341 Building REAL250005052342 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052342' /scratch/stefan/7921156/working/building/REAL250005052342 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052342 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052342/0 /scratch/stefan/7921156/working/building/REAL250005052342 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/474 `/scratch/stefan/7921156/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN(C)C=N1) `REAL250005052342.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052342 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN(C)C=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.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 8, 5, 1, 8, 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, 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] 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: [75, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 75, 111, 111, 111, 143, 143, 143, 143, 143, 75, 75, 75, 75, 32, 32, 9, 1, 111, 143, 143, 143, 143] 143 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: 461 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052342 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN(C)C=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.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 8, 5, 1, 8, 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, 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] 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: [27, 6, 27, 78, 134, 134, 134, 143, 143, 143, 143, 143, 6, 1, 6, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 78, 78, 134, 143, 6, 2, 2, 2, 1] 143 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: 518 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052342 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052342 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052342/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052342 Building REAL250005052343 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052343' /scratch/stefan/7921156/working/building/REAL250005052343 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052343 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052343/0 /scratch/stefan/7921156/working/building/REAL250005052343 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/475 `/scratch/stefan/7921156/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1(F)F) `REAL250005052343.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052343 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 79, 121, 121, 121, 201, 201, 201, 201, 79, 79, 79, 79, 29, 29, 10, 1, 121, 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]) total number of confs: 713 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052343 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 13, 50, 137, 193, 193, 193, 201, 201, 201, 201, 201, 13, 1, 13, 1, 1, 1, 1, 1, 50, 50, 50, 50, 137, 137, 193, 201, 13, 1, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 746 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052343 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052343 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052343/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052343 Building REAL250005052344 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052344' /scratch/stefan/7921156/working/building/REAL250005052344 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052344 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052344/0 /scratch/stefan/7921156/working/building/REAL250005052344 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/476 `/scratch/stefan/7921156/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052344.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052344 none CCC(C)=CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 146, 146, 115, 115, 115, 63, 21, 62, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 146, 146, 146, 146, 115, 63, 63, 63, 63, 21, 21, 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: 861 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052344 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052344 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052344/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052344 Building REAL250005052345 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052345' /scratch/stefan/7921156/working/building/REAL250005052345 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052345 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052345/0 /scratch/stefan/7921156/working/building/REAL250005052345 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/477 `/scratch/stefan/7921156/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C#CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052345.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052345 none CC(C)C#CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 78, 78, 78, 65, 31, 65, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 78, 78, 65, 65, 65, 65, 31, 31, 9, 1] 78 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052345 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052345 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052345/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052345 Building REAL250005052346 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052346' /scratch/stefan/7921156/working/building/REAL250005052346 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052346 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052346/0 /scratch/stefan/7921156/working/building/REAL250005052346 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/478 `/scratch/stefan/7921156/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(O)CCC1) `REAL250005052346.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052346 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 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, 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: [75, 25, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 77, 111, 111, 111, 183, 201, 201, 201, 201, 77, 77, 77, 77, 25, 25, 10, 1, 111, 183, 183, 603, 201, 201, 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: 1433 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: REAL250005052346 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 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, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [65, 30, 65, 149, 197, 197, 197, 201, 201, 201, 201, 201, 30, 8, 30, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 149, 149, 197, 201, 30, 8, 8, 6, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 788 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052346 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052346 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052346/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052346 Building REAL250005052347 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052347' /scratch/stefan/7921156/working/building/REAL250005052347 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052347 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052347/0 /scratch/stefan/7921156/working/building/REAL250005052347 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/479 `/scratch/stefan/7921156/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CNN=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052347.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052347 none CC1=CNN=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 57, 97, 97, 97, 104, 104, 104, 104, 104, 2, 2, 2, 1, 1, 5, 16, 16, 16, 16, 57, 57, 97, 104] 104 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 371 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: REAL250005052347 none CC1=CNN=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 104, 104, 104, 104, 104, 71, 28, 70, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 104, 71, 71, 71, 71, 28, 28, 9, 1] 104 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: 386 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052347 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052347 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052347/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052347 Building REAL250005052348 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052348' /scratch/stefan/7921156/working/building/REAL250005052348 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052348 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052348/0 /scratch/stefan/7921156/working/building/REAL250005052348 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/480 `/scratch/stefan/7921156/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)=C1CCC1) `REAL250005052348.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052348 none CC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 79, 31, 77, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 125, 79, 79, 79, 79, 31, 31, 9, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 686 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: REAL250005052348 none CC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 11, 11, 11, 45, 45, 133, 196, 196, 196, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 11, 45, 45, 45, 45, 133, 133, 196, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 34, 17, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 748 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052348 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052348 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052348/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052348 Building REAL250005052349 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052349' /scratch/stefan/7921156/working/building/REAL250005052349 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052349 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052349/0 /scratch/stefan/7921156/working/building/REAL250005052349 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/481 `/scratch/stefan/7921156/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C#CC1CC1) `REAL250005052349.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052349 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 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, 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] 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: [57, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 57, 78, 78, 78, 78, 78, 78, 78, 57, 57, 57, 57, 26, 26, 8, 1, 78, 78, 78, 78, 78, 78] 78 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: 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: REAL250005052349 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 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, 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] 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: [7, 1, 7, 35, 74, 74, 74, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 35, 35, 74, 78, 1, 1, 1, 1, 1, 1] 78 rigid atoms, others: [32, 1, 33, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 256 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052349 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052349 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052349/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052349 Building REAL250005052350 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052350' /scratch/stefan/7921156/working/building/REAL250005052350 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052350 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052350/0 /scratch/stefan/7921156/working/building/REAL250005052350 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/482 `/scratch/stefan/7921156/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C#CC(C)(C)C) `REAL250005052350.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052350 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C#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.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [68, 29, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 68, 87, 87, 87, 87, 87, 87, 87, 87, 68, 68, 68, 68, 29, 29, 8, 1, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87] 87 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: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052350 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052350 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052350/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052350 Building REAL250005052351 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052351' /scratch/stefan/7921156/working/building/REAL250005052351 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052351 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052351/0 /scratch/stefan/7921156/working/building/REAL250005052351 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/483 `/scratch/stefan/7921156/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1[N+](=O)[O-]) `REAL250005052351.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052351 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1[N+](=O)[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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 64, 106, 106, 106, 201, 201, 201, 201, 201, 201, 201, 64, 64, 64, 64, 23, 23, 7, 1, 106, 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]) total number of confs: 689 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052351 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1[N+](=O)[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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 11, 37, 118, 181, 181, 181, 201, 201, 201, 201, 201, 11, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 118, 118, 181, 201, 11, 1, 1] 201 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 718 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052351 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052351 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052351/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052351 Building REAL250005052352 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052352' /scratch/stefan/7921156/working/building/REAL250005052352 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052352 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052352/0 /scratch/stefan/7921156/working/building/REAL250005052352 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/484 `/scratch/stefan/7921156/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052352.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052352 none COCCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 192, 109, 109, 109, 72, 24, 70, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 192, 192, 109, 72, 72, 72, 72, 24, 24, 8, 1] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 834 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052352 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052352 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052352/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052352 Building REAL250005052353 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052353' /scratch/stefan/7921156/working/building/REAL250005052353 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052353 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052353/0 /scratch/stefan/7921156/working/building/REAL250005052353 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/485 `/scratch/stefan/7921156/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1) `REAL250005052353.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052353 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 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: [78, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 79, 102, 102, 102, 172, 172, 79, 79, 79, 79, 33, 33, 10, 1, 102, 172, 172, 172, 172, 172] 172 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: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052353 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 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: [47, 11, 47, 111, 159, 159, 159, 172, 172, 172, 172, 172, 11, 1, 11, 1, 1, 1, 47, 47, 47, 47, 111, 111, 159, 172, 11, 1, 1, 1, 1, 1] 172 rigid atoms, others: [13, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 612 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052353 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052353 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052353/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052353 Building REAL250005052354 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052354' /scratch/stefan/7921156/working/building/REAL250005052354 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052354 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052354/0 /scratch/stefan/7921156/working/building/REAL250005052354 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/486 `/scratch/stefan/7921156/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC1) `REAL250005052354.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052354 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [80, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 82, 109, 109, 109, 195, 195, 195, 82, 82, 82, 82, 34, 34, 10, 1, 109, 195, 195, 195, 195, 195, 195, 195] 195 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: 684 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052354 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [40, 11, 40, 116, 182, 182, 182, 195, 195, 195, 195, 195, 11, 1, 11, 1, 1, 1, 1, 40, 40, 40, 40, 116, 116, 182, 195, 11, 1, 1, 1, 1, 1, 1, 1] 195 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 696 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052354 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052354 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052354/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052354 Building REAL250005052355 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052355' /scratch/stefan/7921156/working/building/REAL250005052355 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052355 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052355/0 /scratch/stefan/7921156/working/building/REAL250005052355 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/487 `/scratch/stefan/7921156/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCC1) `REAL250005052355.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052355 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [67, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 110, 110, 110, 187, 187, 187, 187, 69, 69, 69, 69, 27, 27, 9, 1, 110, 187, 187, 187, 187, 187, 187, 187, 187, 187] 187 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: 648 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: REAL250005052355 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [36, 9, 36, 105, 178, 178, 178, 187, 187, 187, 187, 187, 9, 1, 9, 1, 1, 1, 1, 1, 36, 36, 36, 36, 105, 105, 178, 187, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 187 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 661 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052355 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052355 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052355/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052355 Building REAL250005052356 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052356' /scratch/stefan/7921156/working/building/REAL250005052356 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052356 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052356/0 /scratch/stefan/7921156/working/building/REAL250005052356 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/488 `/scratch/stefan/7921156/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCOCC1) `REAL250005052356.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052356 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 5, 12, 5, 5, 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, 7, 7, 3, 7, 3, 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, 7] 0 hydrogens 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, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 78, 127, 127, 127, 201, 201, 201, 201, 201, 78, 78, 78, 78, 30, 30, 9, 1, 127, 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]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052356 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 5, 12, 5, 5, 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, 7, 7, 3, 7, 3, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 13, 50, 131, 193, 193, 193, 201, 201, 201, 201, 201, 13, 1, 13, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 131, 131, 193, 201, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 739 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052356 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052356 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052356/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052356 Building REAL250005052357 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052357' /scratch/stefan/7921156/working/building/REAL250005052357 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052357 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052357/0 /scratch/stefan/7921156/working/building/REAL250005052357 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/489 `/scratch/stefan/7921156/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN(C)N=C1) `REAL250005052357.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052357 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN(C)N=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.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 8, 5, 8, 1, 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, 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] 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: [69, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 100, 100, 100, 101, 101, 101, 101, 101, 69, 69, 69, 69, 34, 34, 9, 1, 100, 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]) total number of confs: 368 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052357 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN(C)N=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.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 8, 5, 8, 1, 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, 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] 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: [16, 5, 16, 54, 96, 96, 96, 101, 101, 101, 101, 101, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 54, 54, 96, 101, 5, 2, 2, 2, 1] 101 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: 360 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052357 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052357 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052357/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052357 Building REAL250005052358 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052358' /scratch/stefan/7921156/working/building/REAL250005052358 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052358 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052358/0 /scratch/stefan/7921156/working/building/REAL250005052358 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/490 `/scratch/stefan/7921156/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005052358.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052358 none CCC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 15, 15, 15, 15, 9, 15, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 16, 16, 16, 16, 16, 15, 15, 15, 15, 15, 15, 9, 9, 4, 1, 15, 15, 15, 15, 15, 15] 16 rigid atoms, others: [36, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052358 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052358 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052358/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052358 Building REAL250005052359 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052359' /scratch/stefan/7921156/working/building/REAL250005052359 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052359 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052359/0 /scratch/stefan/7921156/working/building/REAL250005052359 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/491 `/scratch/stefan/7921156/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)CO1) `REAL250005052359.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052359 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 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, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [70, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 72, 112, 112, 112, 138, 138, 138, 138, 138, 72, 72, 72, 72, 28, 28, 9, 1, 112, 138, 138, 138, 138, 138, 138, 138, 138, 138] 138 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: 515 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052359 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 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, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [33, 11, 33, 91, 135, 135, 135, 138, 138, 138, 138, 138, 11, 1, 11, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 91, 91, 135, 138, 11, 1, 1, 1, 1, 2, 2, 2, 1, 1] 138 rigid atoms, others: [32, 33, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 501 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052359 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052359 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052359/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052359 Building REAL250005052360 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052360' /scratch/stefan/7921156/working/building/REAL250005052360 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052360 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052360/0 /scratch/stefan/7921156/working/building/REAL250005052360 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/492 `/scratch/stefan/7921156/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1CCC2) `REAL250005052360.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052360 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1CCC2 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [81, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 83, 117, 117, 117, 197, 197, 197, 197, 197, 197, 83, 83, 83, 83, 29, 29, 8, 1, 117, 197, 197, 197, 197, 197, 197, 197, 197] 197 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: 563 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: REAL250005052360 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1CCC2 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [31, 6, 31, 112, 186, 186, 186, 197, 197, 197, 197, 197, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 112, 112, 186, 197, 6, 1, 1, 1, 1, 1, 1, 1, 1] 197 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 690 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052360 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052360 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052360/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052360 Building REAL250005052361 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052361' /scratch/stefan/7921156/working/building/REAL250005052361 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052361 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052361/0 /scratch/stefan/7921156/working/building/REAL250005052361 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/493 `/scratch/stefan/7921156/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC(=O)N1) `REAL250005052361.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052361 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [63, 27, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 65, 101, 101, 101, 150, 150, 150, 150, 150, 150, 65, 65, 65, 65, 26, 26, 8, 1, 101, 150, 150, 150, 150, 150] 150 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: 536 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052361 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 11, 36, 99, 142, 142, 142, 150, 150, 150, 150, 150, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 99, 99, 142, 150, 11, 1, 1, 1, 1, 1] 150 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 556 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052361 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052361 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052361/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052361 Building REAL250005052362 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052362' /scratch/stefan/7921156/working/building/REAL250005052362 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052362 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052362/0 /scratch/stefan/7921156/working/building/REAL250005052362 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/494 `/scratch/stefan/7921156/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@H+](C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052362.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052362 none CCC[N@H+](C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 20, 19, 13, 19, 19, 12, 12, 12, 12, 6, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 20, 20, 19, 19, 19, 13, 13, 12, 12, 12, 12, 12, 6, 6, 2, 1] 22 rigid atoms, others: [42, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052362 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052362/1 /scratch/stefan/7921156/working/building/REAL250005052362 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/495 `/scratch/stefan/7921156/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@@H+](C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052362.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052362/1/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: REAL250005052362 none CCC[N@@H+](C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 21, 21, 16, 21, 21, 15, 15, 15, 14, 7, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 16, 16, 15, 14, 14, 14, 14, 7, 7, 2, 1] 24 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: 117 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052362 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052362 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052362/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052362/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052362 Building REAL250005052363 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052363' /scratch/stefan/7921156/working/building/REAL250005052363 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052363 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052363/0 /scratch/stefan/7921156/working/building/REAL250005052363 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/496 `/scratch/stefan/7921156/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC(C)(C)C) `REAL250005052363.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052363 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 24, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 68, 104, 104, 104, 201, 201, 201, 201, 201, 68, 68, 68, 68, 24, 24, 8, 1, 104, 201, 201, 201, 201, 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, 41, 42]) total number of confs: 825 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052363 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052363 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052363/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052363 Building REAL250005052364 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052364' /scratch/stefan/7921156/working/building/REAL250005052364 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052364 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052364/0 /scratch/stefan/7921156/working/building/REAL250005052364 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/497 `/scratch/stefan/7921156/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NC=N1) `REAL250005052364.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052364 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NC=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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [67, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 68, 95, 95, 95, 97, 97, 97, 97, 97, 68, 68, 68, 68, 32, 32, 9, 1, 95, 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]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052364 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NC=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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 54, 88, 88, 88, 97, 97, 97, 97, 97, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 54, 54, 88, 97, 6, 1, 1, 1] 97 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052364 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052364 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052364/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052364 Building REAL250005052365 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052365' /scratch/stefan/7921156/working/building/REAL250005052365 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052365 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052365/0 /scratch/stefan/7921156/working/building/REAL250005052365 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/498 `/scratch/stefan/7921156/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CC=CO1) `REAL250005052365.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052365 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 1, 1, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 54, 54, 54, 140, 201, 201, 201, 201, 35, 35, 35, 35, 14, 14, 4, 1, 54, 140, 140, 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: 651 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052365 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 1, 1, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 34, 71, 140, 201, 201, 201, 201, 201, 201, 201, 201, 34, 5, 34, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 140, 140, 201, 201, 34, 5, 5, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 800 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052365 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052365 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052365/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052365 Building REAL250005052366 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052366' /scratch/stefan/7921156/working/building/REAL250005052366 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052366 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052366/0 /scratch/stefan/7921156/working/building/REAL250005052366 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/499 `/scratch/stefan/7921156/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=CC=N1) `REAL250005052366.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052366 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=CC=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.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 7, 3, 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, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 53, 72, 72, 72, 72, 72, 72, 72, 72, 53, 53, 53, 53, 25, 25, 9, 1, 72, 72, 72, 72] 72 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]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052366 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=CC=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.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 7, 3, 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: [23, 7, 23, 47, 68, 68, 68, 72, 72, 72, 72, 72, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 47, 47, 68, 72, 7, 1, 1, 1] 72 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052366 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052366 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052366/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052366 Building REAL250005052367 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052367' /scratch/stefan/7921156/working/building/REAL250005052367 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052367 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052367/0 /scratch/stefan/7921156/working/building/REAL250005052367 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/500 `/scratch/stefan/7921156/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052367.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052367 none CCC(C)CCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 196, 134, 196, 115, 32, 32, 32, 28, 14, 28, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 196, 197, 196, 197, 149, 149, 115, 115, 32, 28, 28, 28, 28, 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: 1013 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052367 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052367 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052367/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052367 Building REAL250005052368 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052368' /scratch/stefan/7921156/working/building/REAL250005052368 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052368 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052368/0 /scratch/stefan/7921156/working/building/REAL250005052368 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/501 `/scratch/stefan/7921156/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CN=N1) `REAL250005052368.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052368 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CN=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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [78, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 79, 103, 103, 103, 109, 109, 109, 109, 109, 79, 79, 79, 79, 34, 34, 9, 1, 103, 109, 109, 109] 109 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]) total number of confs: 410 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052368 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=CN=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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [19, 6, 19, 63, 100, 100, 100, 109, 109, 109, 109, 109, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 63, 63, 100, 109, 6, 1, 1, 1] 109 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 380 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052368 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052368 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052368/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052368 Building REAL250005052369 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052369' /scratch/stefan/7921156/working/building/REAL250005052369 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052369 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052369/0 /scratch/stefan/7921156/working/building/REAL250005052369 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/502 `/scratch/stefan/7921156/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCOC1C) `REAL250005052369.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052369 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCOC1C NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 5, 12, 5, 5, 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, 7, 7, 3, 7, 3, 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, 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: [48, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 50, 67, 67, 67, 70, 70, 70, 70, 70, 50, 50, 50, 50, 23, 23, 9, 1, 67, 70, 70, 70, 70, 70, 70, 70, 70, 70] 70 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: 267 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: REAL250005052369 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCOC1C NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 5, 12, 5, 5, 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, 7, 7, 3, 7, 3, 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, 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: [12, 4, 12, 39, 66, 66, 66, 70, 70, 70, 70, 70, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 39, 39, 66, 70, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2] 70 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38]) total number of confs: 244 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052369 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052369 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052369/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052369 Building REAL250005052370 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052370' /scratch/stefan/7921156/working/building/REAL250005052370 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052370 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052370/0 /scratch/stefan/7921156/working/building/REAL250005052370 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/503 `/scratch/stefan/7921156/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CCOC1) `REAL250005052370.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052370 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 12, 5, 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, 7, 7, 3, 7, 3, 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, 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: [62, 25, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 64, 94, 94, 94, 144, 144, 144, 144, 144, 64, 64, 64, 64, 25, 25, 10, 1, 94, 144, 144, 144, 144, 144, 144, 144, 144, 144] 144 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: 505 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052370 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 12, 5, 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, 7, 7, 3, 7, 3, 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, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 23, 84, 138, 138, 138, 144, 144, 144, 144, 144, 5, 1, 5, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 84, 84, 138, 144, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1] 144 rigid atoms, others: [33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 508 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052370 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052370 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052370/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052370 Building REAL250005052371 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052371' /scratch/stefan/7921156/working/building/REAL250005052371 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052371 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052371/0 /scratch/stefan/7921156/working/building/REAL250005052371 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/504 `/scratch/stefan/7921156/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052371.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052371 none CCC(CC)CC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 161, 114, 159, 194, 31, 31, 31, 27, 12, 27, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 187, 187, 187, 185, 187, 163, 193, 191, 194, 194, 194, 114, 114, 31, 27, 27, 27, 27, 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: 1049 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052371 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052371 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052371/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052371 Building REAL250005052372 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052372' /scratch/stefan/7921156/working/building/REAL250005052372 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052372 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052372/0 /scratch/stefan/7921156/working/building/REAL250005052372 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/505 `/scratch/stefan/7921156/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052372.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052372 none CCC(C)C(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 156, 183, 77, 156, 77, 77, 63, 23, 62, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 188, 188, 188, 188, 156, 156, 156, 156, 77, 63, 63, 63, 63, 23, 23, 5, 1] 201 rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 923 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052372 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052372 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052372/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052372 Building REAL250005052373 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052373' /scratch/stefan/7921156/working/building/REAL250005052373 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052373 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052373/0 /scratch/stefan/7921156/working/building/REAL250005052373 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/506 `/scratch/stefan/7921156/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CC)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052373.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052373 none CCCC(CC)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 176, 130, 56, 130, 156, 56, 56, 40, 17, 39, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 189, 189, 189, 186, 189, 179, 179, 130, 167, 167, 167, 167, 167, 56, 40, 40, 40, 40, 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: 1165 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052373 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052373 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052373/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052373 Building REAL250005052374 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052374' /scratch/stefan/7921156/working/building/REAL250005052374 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052374 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052374/0 /scratch/stefan/7921156/working/building/REAL250005052374 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/507 `/scratch/stefan/7921156/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C)CC1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052374.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052374 none CCC1(C)CC1C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 25, 94, 179, 179, 179, 191, 191, 191, 191, 191, 3, 3, 3, 2, 2, 2, 2, 2, 1, 1, 1, 6, 25, 25, 25, 25, 94, 94, 179, 191] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 657 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: REAL250005052374 none CCC1(C)CC1C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 191, 191, 191, 128, 128, 128, 78, 27, 76, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 191, 191, 191, 191, 191, 128, 78, 78, 78, 78, 27, 27, 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: 746 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052374 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052374 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052374/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052374 Building REAL250005052375 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052375' /scratch/stefan/7921156/working/building/REAL250005052375 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052375 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052375/0 /scratch/stefan/7921156/working/building/REAL250005052375 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/508 `/scratch/stefan/7921156/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052375.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052375 none COCC(C)CC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 152, 103, 154, 22, 22, 22, 22, 10, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 201, 157, 157, 157, 157, 103, 103, 22, 22, 22, 22, 22, 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: 951 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052375 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052375 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052375/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052375 Building REAL250005052376 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052376' /scratch/stefan/7921156/working/building/REAL250005052376 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052376 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052376/0 /scratch/stefan/7921156/working/building/REAL250005052376 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/509 `/scratch/stefan/7921156/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)NC(=O)C1CCC(F)C1) `REAL250005052376.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052376 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [72, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 74, 123, 123, 123, 201, 201, 201, 201, 201, 74, 74, 74, 74, 30, 30, 9, 1, 123, 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]) total number of confs: 700 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: REAL250005052376 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 12, 42, 132, 191, 191, 191, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 132, 132, 191, 201, 12, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 728 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052376 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052376 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052376/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052376 Building REAL250005052377 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052377' /scratch/stefan/7921156/working/building/REAL250005052377 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052377 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052377/0 /scratch/stefan/7921156/working/building/REAL250005052377 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/510 `/scratch/stefan/7921156/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)NC(=O)CCC1(C)CC1) `REAL250005052377.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052377 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC1(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 42, 63, 63, 63, 142, 152, 201, 201, 201, 42, 42, 42, 42, 17, 17, 4, 1, 63, 142, 142, 155, 155, 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: 847 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: REAL250005052377 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC1(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 35, 83, 150, 201, 201, 201, 201, 201, 201, 201, 201, 35, 7, 35, 5, 1, 1, 1, 1, 1, 83, 83, 83, 83, 150, 150, 201, 201, 35, 7, 7, 5, 5, 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: 822 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052377 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052377 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052377/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052377 Building REAL250005052378 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052378' /scratch/stefan/7921156/working/building/REAL250005052378 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052378 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052378/0 /scratch/stefan/7921156/working/building/REAL250005052378 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/511 `/scratch/stefan/7921156/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)ON=C1) `REAL250005052378.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052378 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)ON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 30, 30, 93, 143, 143, 143, 147, 147, 147, 147, 147, 1, 1, 1, 2, 2, 2, 9, 30, 30, 30, 30, 93, 93, 143, 147, 1] 147 rigid atoms, others: [0, 1, 2, 3, 33, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 551 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: REAL250005052378 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)ON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 125, 125, 125, 83, 30, 82, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 147, 147, 125, 83, 83, 83, 83, 30, 30, 8, 1, 147] 147 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 512 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052378 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052378 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052378/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052378 Building REAL250005052379 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052379' /scratch/stefan/7921156/working/building/REAL250005052379 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052379 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052379/0 /scratch/stefan/7921156/working/building/REAL250005052379 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/512 `/scratch/stefan/7921156/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052379.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052379 none CC[N@H+](C)CCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 13, 18, 18, 13, 10, 10, 10, 9, 6, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 13, 13, 13, 13, 10, 9, 9, 9, 9, 6, 6, 3, 1] 18 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: 83 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052379 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052379/1 /scratch/stefan/7921156/working/building/REAL250005052379 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/513 `/scratch/stefan/7921156/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052379.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052379/1/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: REAL250005052379 none CC[N@@H+](C)CCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 21, 16, 21, 21, 16, 11, 11, 11, 9, 6, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 21, 21, 21, 16, 16, 16, 16, 11, 9, 9, 9, 9, 6, 6, 4, 1] 22 rigid atoms, others: [42, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 104 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052379 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052379 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052379/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052379/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052379 Building REAL250005052380 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052380' /scratch/stefan/7921156/working/building/REAL250005052380 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052380 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052380/0 /scratch/stefan/7921156/working/building/REAL250005052380 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/514 `/scratch/stefan/7921156/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CON=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052380.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052380 none CC1=CON=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 60, 115, 115, 115, 124, 124, 124, 124, 124, 2, 2, 2, 1, 6, 17, 17, 17, 17, 60, 60, 115, 124] 124 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052380 none CC1=CON=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 124, 124, 122, 122, 122, 87, 35, 87, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 122, 87, 87, 87, 87, 35, 35, 9, 1] 124 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: 459 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052380 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052380 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052380/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052380 Building REAL250005052381 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052381' /scratch/stefan/7921156/working/building/REAL250005052381 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052381 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052381/0 /scratch/stefan/7921156/working/building/REAL250005052381 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/515 `/scratch/stefan/7921156/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)NC(=O)CN1N=CN=N1) `REAL250005052381.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052381 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1N=CN=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.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 45, 70, 70, 70, 137, 201, 201, 201, 201, 45, 45, 45, 45, 20, 20, 8, 1, 70, 137, 137, 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]) total number of confs: 661 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052381 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1N=CN=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.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 55, 105, 174, 199, 199, 199, 201, 201, 201, 201, 201, 55, 9, 55, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 174, 174, 199, 201, 55, 9, 9, 1] 201 rigid atoms, others: [32, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 811 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052381 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052381 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052381/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052381 Building REAL250005052382 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052382' /scratch/stefan/7921156/working/building/REAL250005052382 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052382 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052382/0 /scratch/stefan/7921156/working/building/REAL250005052382 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/516 `/scratch/stefan/7921156/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052382.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052382 none CCCC[C@@H](C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 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: [199, 185, 176, 129, 52, 129, 129, 52, 52, 44, 16, 44, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 183, 185, 181, 181, 129, 129, 129, 52, 44, 44, 44, 44, 16, 16, 4, 1] 201 rigid atoms, others: [42, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 950 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052382 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052382 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052382/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052382 Building REAL250005052383 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052383' /scratch/stefan/7921156/working/building/REAL250005052383 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052383 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052383/0 /scratch/stefan/7921156/working/building/REAL250005052383 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/517 `/scratch/stefan/7921156/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052383.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052383 none CCC(C)(C)CC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 166, 76, 166, 166, 37, 37, 37, 31, 17, 31, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 166, 166, 166, 166, 166, 166, 76, 76, 37, 31, 31, 31, 31, 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: 955 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052383 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052383 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052383/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052383 Building REAL250005052384 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052384' /scratch/stefan/7921156/working/building/REAL250005052384 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052384 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052384/0 /scratch/stefan/7921156/working/building/REAL250005052384 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/518 `/scratch/stefan/7921156/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052384.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052384 none CC(C)C(C)(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [131, 119, 132, 66, 118, 119, 66, 66, 46, 17, 46, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 133, 133, 119, 118, 119, 119, 119, 119, 66, 46, 46, 46, 46, 17, 17, 4, 1] 133 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: 600 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052384 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052384 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052384/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052384 Building REAL250005052385 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052385' /scratch/stefan/7921156/working/building/REAL250005052385 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052385 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052385/0 /scratch/stefan/7921156/working/building/REAL250005052385 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/519 `/scratch/stefan/7921156/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052385.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052385 none C=CC(C)(C)CC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 104, 198, 200, 44, 44, 44, 36, 15, 36, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 104, 44, 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: 916 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052385 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052385 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052385/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052385 Building REAL250005052386 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052386' /scratch/stefan/7921156/working/building/REAL250005052386 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052386 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052386/0 /scratch/stefan/7921156/working/building/REAL250005052386 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/520 `/scratch/stefan/7921156/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1N=CC=N1) `REAL250005052386.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052386 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1N=CC=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.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 8, 1, 1, 8, 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, 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] 0 hydrogens 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, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 71, 113, 113, 113, 193, 201, 201, 201, 201, 71, 71, 71, 71, 25, 25, 8, 1, 113, 193, 193, 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: 799 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052386 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1N=CC=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.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 8, 1, 1, 8, 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, 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] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [72, 31, 72, 145, 173, 173, 173, 184, 184, 184, 184, 184, 31, 5, 31, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 145, 145, 173, 184, 31, 5, 5, 1, 1] 184 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 729 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052386 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052386 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052386/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052386 Building REAL250005052387 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052387' /scratch/stefan/7921156/working/building/REAL250005052387 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052387 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052387/0 /scratch/stefan/7921156/working/building/REAL250005052387 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/521 `/scratch/stefan/7921156/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052387.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052387 none C=CCCCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 114, 35, 35, 35, 25, 13, 25, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 189, 188, 142, 142, 114, 114, 35, 25, 25, 25, 25, 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: 981 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052387 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052387 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052387/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052387 Building REAL250005052388 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052388' /scratch/stefan/7921156/working/building/REAL250005052388 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052388 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052388/0 /scratch/stefan/7921156/working/building/REAL250005052388 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/522 `/scratch/stefan/7921156/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052388.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052388 none CCC(C)(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 179, 104, 179, 179, 104, 104, 71, 31, 69, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 179, 179, 179, 179, 179, 179, 104, 71, 71, 71, 71, 31, 31, 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: 1011 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052388 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052388 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052388/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052388 Building REAL250005052389 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052389' /scratch/stefan/7921156/working/building/REAL250005052389 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052389 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052389/0 /scratch/stefan/7921156/working/building/REAL250005052389 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/523 `/scratch/stefan/7921156/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052389.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052389 none CCCC(C)(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 165, 93, 165, 165, 93, 93, 57, 19, 55, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 165, 165, 165, 165, 165, 165, 93, 57, 57, 57, 57, 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: 920 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052389 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052389 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052389/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052389 Building REAL250005052390 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052390' /scratch/stefan/7921156/working/building/REAL250005052390 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052390 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052390/0 /scratch/stefan/7921156/working/building/REAL250005052390 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/524 `/scratch/stefan/7921156/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)NC(=O)C1(C(N)=O)CC1) `REAL250005052390.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052390 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C(N)=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.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 56, 104, 104, 104, 185, 201, 201, 185, 185, 56, 56, 56, 56, 19, 19, 6, 1, 104, 201, 201, 185, 185, 185, 185] 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: 677 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: REAL250005052390 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C(N)=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.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 7, 26, 88, 174, 174, 174, 185, 185, 185, 185, 185, 7, 1, 7, 1, 1, 7, 7, 1, 1, 26, 26, 26, 26, 88, 88, 174, 185, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 629 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052390 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052390 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052390/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052390 Building REAL250005052391 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052391' /scratch/stefan/7921156/working/building/REAL250005052391 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052391 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052391/0 /scratch/stefan/7921156/working/building/REAL250005052391 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/525 `/scratch/stefan/7921156/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)NC(=O)C(N)=O) `REAL250005052391.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052391 none 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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6] dock color type numbers: [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] 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: [56, 27, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 56, 76, 76, 76, 81, 81, 56, 56, 56, 56, 27, 27, 8, 1, 76, 81, 81] 81 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]) total number of confs: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052391 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052391 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052391/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052391 Building REAL250005052392 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052392' /scratch/stefan/7921156/working/building/REAL250005052392 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052392 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052392/0 /scratch/stefan/7921156/working/building/REAL250005052392 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/526 `/scratch/stefan/7921156/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052392.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052392 none CC1=NOC=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 25, 25, 59, 85, 85, 85, 90, 90, 90, 90, 90, 2, 2, 2, 1, 9, 25, 25, 25, 25, 59, 59, 85, 90] 90 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052392 none CC1=NOC=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 73, 73, 73, 51, 20, 51, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 73, 51, 51, 51, 51, 20, 20, 9, 1] 90 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: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052392 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052392 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052392/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052392 Building REAL250005052393 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052393' /scratch/stefan/7921156/working/building/REAL250005052393 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052393 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052393/0 /scratch/stefan/7921156/working/building/REAL250005052393 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/527 `/scratch/stefan/7921156/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)NC(=O)C1(C)CC=CC1) `REAL250005052393.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052393 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 1, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [72, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 74, 106, 106, 106, 152, 152, 152, 152, 152, 74, 74, 74, 74, 32, 32, 10, 1, 106, 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]) total number of confs: 547 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: REAL250005052393 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 1, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [21, 5, 21, 82, 139, 139, 139, 152, 152, 152, 152, 152, 5, 1, 5, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 82, 82, 139, 152, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1] 152 rigid atoms, others: [33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 522 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052393 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052393 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052393/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052393 Building REAL250005052394 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052394' /scratch/stefan/7921156/working/building/REAL250005052394 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052394 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052394/0 /scratch/stefan/7921156/working/building/REAL250005052394 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/528 `/scratch/stefan/7921156/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005052394.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052394 none COC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [167, 155, 104, 104, 104, 57, 18, 54, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 155, 201, 201, 167, 167, 167, 155, 104, 57, 57, 57, 57, 18, 18, 4, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 944 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052394 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052394 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052394/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052394 Building REAL250005052395 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052395' /scratch/stefan/7921156/working/building/REAL250005052395 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052395 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052395/0 /scratch/stefan/7921156/working/building/REAL250005052395 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/529 `/scratch/stefan/7921156/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC1C) `REAL250005052395.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052395 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 65, 65, 65, 169, 201, 201, 201, 45, 45, 45, 45, 17, 17, 4, 1, 65, 169, 169, 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: 795 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052395 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 42, 88, 162, 201, 201, 201, 201, 201, 201, 201, 201, 42, 6, 42, 1, 1, 1, 1, 1, 88, 88, 88, 88, 162, 162, 201, 201, 42, 6, 6, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 826 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052395 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052395 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052395/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052395 Building REAL250005052396 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052396' /scratch/stefan/7921156/working/building/REAL250005052396 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052396 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052396/0 /scratch/stefan/7921156/working/building/REAL250005052396 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/530 `/scratch/stefan/7921156/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(CC)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052396.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052396 none C=CC(C)(CC)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 173, 97, 173, 172, 195, 97, 97, 55, 17, 54, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 193, 193, 193, 173, 173, 173, 201, 201, 201, 201, 201, 97, 55, 55, 55, 55, 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: 981 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052396 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052396 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052396/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052396 Building REAL250005052397 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052397' /scratch/stefan/7921156/working/building/REAL250005052397 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052397 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052397/0 /scratch/stefan/7921156/working/building/REAL250005052397 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/531 `/scratch/stefan/7921156/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[C@H]1CCOC1) `REAL250005052397.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052397 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['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', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7] 0 hydrogens 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, 48, 65, 65, 65, 163, 201, 201, 201, 201, 201, 48, 48, 48, 48, 17, 17, 4, 1, 65, 163, 163, 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]) total number of confs: 822 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052397 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['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', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7] 0 hydrogens 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, 37, 81, 157, 201, 201, 201, 201, 201, 201, 201, 201, 37, 7, 37, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 157, 157, 201, 201, 37, 7, 7, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 797 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052397 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052397 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052397/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052397 Building REAL250005052398 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052398' /scratch/stefan/7921156/working/building/REAL250005052398 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052398 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052398/0 /scratch/stefan/7921156/working/building/REAL250005052398 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/532 `/scratch/stefan/7921156/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005052398.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052398 none CCC1(C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 103, 168, 170, 170, 171, 171, 171, 171, 171, 1, 1, 4, 4, 4, 4, 4, 7, 32, 32, 32, 32, 103, 103, 170, 171, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 36, 37, 35, 34, 18, 19] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 641 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: REAL250005052398 none CCC1(C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 80, 80, 80, 55, 18, 54, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 171, 171, 201, 201, 201, 201, 201, 80, 55, 55, 55, 55, 18, 18, 5, 1, 171, 171, 171, 171] 201 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 733 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052398 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052398 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052398/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052398 Building REAL250005052399 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052399' /scratch/stefan/7921156/working/building/REAL250005052399 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052399 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052399/0 /scratch/stefan/7921156/working/building/REAL250005052399 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/533 `/scratch/stefan/7921156/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)C) `REAL250005052399.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052399 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [57, 28, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 59, 71, 71, 71, 78, 78, 78, 59, 59, 59, 59, 28, 28, 9, 1, 71, 78, 78, 78, 78, 78, 78, 78, 78, 78] 78 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, 36]) total number of confs: 321 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052399 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052399 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052399/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052399 Building REAL250005052400 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052400' /scratch/stefan/7921156/working/building/REAL250005052400 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052400 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052400/0 /scratch/stefan/7921156/working/building/REAL250005052400 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/534 `/scratch/stefan/7921156/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=NNC=N1) `REAL250005052400.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052400 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=NNC=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.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', '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, 1, 11, 5, 1, 8, 8, 1, 8, 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, 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] 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, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 34, 43, 43, 43, 69, 112, 112, 112, 112, 34, 34, 34, 34, 21, 21, 7, 1, 43, 69, 69, 112, 112] 112 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: 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: REAL250005052400 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=NNC=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.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', '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, 1, 11, 5, 1, 8, 8, 1, 8, 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, 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] 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: [65, 42, 65, 94, 110, 110, 110, 112, 112, 112, 112, 112, 42, 9, 42, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 94, 94, 110, 112, 42, 9, 9, 1, 1] 112 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 435 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052400 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052400/1 /scratch/stefan/7921156/working/building/REAL250005052400 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/535 `/scratch/stefan/7921156/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=NN=CN1) `REAL250005052400.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052400/1/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: REAL250005052400 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=NN=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.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [52, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 53, 89, 89, 89, 150, 155, 155, 155, 155, 53, 53, 53, 53, 23, 23, 9, 1, 89, 150, 150, 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: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052400 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=NN=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.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [60, 29, 60, 110, 147, 147, 147, 155, 155, 155, 155, 155, 29, 7, 29, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 110, 110, 147, 155, 29, 7, 7, 1, 1] 155 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 609 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052400 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052400 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052400/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052400/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052400 Building REAL250005052401 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052401' /scratch/stefan/7921156/working/building/REAL250005052401 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052401 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052401/0 /scratch/stefan/7921156/working/building/REAL250005052401 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/536 `/scratch/stefan/7921156/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052401.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052401 none C=C(C)CCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 187, 85, 85, 85, 62, 27, 62, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 187, 187, 85, 62, 62, 62, 62, 27, 27, 8, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 883 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052401 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052401 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052401/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052401 Building REAL250005052402 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052402' /scratch/stefan/7921156/working/building/REAL250005052402 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052402 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052402/0 /scratch/stefan/7921156/working/building/REAL250005052402 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/537 `/scratch/stefan/7921156/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)NC(=O)C1=CC=NS1) `REAL250005052402.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052402 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', '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, 1, 11, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [54, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 55, 78, 78, 78, 98, 98, 98, 98, 55, 55, 55, 55, 24, 24, 9, 1, 78, 98, 98] 98 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]) 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: REAL250005052402 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', '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, 1, 11, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [26, 7, 26, 64, 95, 95, 95, 98, 98, 98, 98, 98, 7, 1, 7, 1, 1, 1, 1, 1, 26, 26, 26, 26, 64, 64, 95, 98, 8, 1, 1] 98 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 359 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052402 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052402 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052402/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052402 Building REAL250005052403 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052403' /scratch/stefan/7921156/working/building/REAL250005052403 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052403 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052403/0 /scratch/stefan/7921156/working/building/REAL250005052403 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/538 `/scratch/stefan/7921156/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(C)(F)F) `REAL250005052403.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052403 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 0 hydrogens 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, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 52, 86, 86, 86, 157, 197, 201, 201, 52, 52, 52, 52, 21, 21, 6, 1, 86, 157, 157, 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]) total number of confs: 908 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052403 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052403 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052403/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052403 Building REAL250005052404 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052404' /scratch/stefan/7921156/working/building/REAL250005052404 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052404 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052404/0 /scratch/stefan/7921156/working/building/REAL250005052404 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/539 `/scratch/stefan/7921156/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005052404.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052404 none CCCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 7, 7, 7, 25, 25, 71, 149, 149, 149, 157, 157, 157, 157, 157, 1, 1, 9, 9, 9, 9, 9, 5, 5, 7, 25, 25, 25, 25, 71, 71, 149, 157, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 37, 38, 39, 40, 19, 20] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 554 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: REAL250005052404 none CCCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 184, 157, 80, 80, 80, 53, 18, 52, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 157, 157, 201, 201, 201, 201, 201, 184, 184, 80, 53, 53, 53, 53, 18, 18, 5, 1, 157, 157, 157, 157] 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: 796 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052404 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052404 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052404/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052404 Building REAL250005052405 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052405' /scratch/stefan/7921156/working/building/REAL250005052405 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052405 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052405/0 /scratch/stefan/7921156/working/building/REAL250005052405 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/540 `/scratch/stefan/7921156/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H]1C[C@H]1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052405.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052405 none CCC[C@@H]1C[C@H]1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 31, 31, 77, 125, 125, 125, 132, 132, 132, 132, 132, 13, 13, 13, 13, 13, 7, 7, 1, 1, 12, 31, 31, 31, 31, 77, 77, 125, 132] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 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: REAL250005052405 none CCC[C@@H]1C[C@H]1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 132, 132, 132, 132, 38, 132, 38, 38, 28, 13, 28, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 196, 196, 132, 132, 38, 28, 28, 28, 28, 12, 12, 3, 1] 201 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 799 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052405 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052405 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052405/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052405 Building REAL250005052406 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052406' /scratch/stefan/7921156/working/building/REAL250005052406 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052406 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052406/0 /scratch/stefan/7921156/working/building/REAL250005052406 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/541 `/scratch/stefan/7921156/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005052406.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052406 none CC(C)C1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 1, 1, 7, 7, 7, 27, 27, 96, 184, 184, 184, 192, 192, 192, 192, 192, 1, 1, 10, 10, 10, 10, 10, 10, 10, 7, 27, 27, 27, 27, 96, 96, 184, 192, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 37, 38, 39, 40, 19, 20] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 685 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: REAL250005052406 none CC(C)C1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 201, 105, 105, 105, 68, 27, 66, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 192, 192, 201, 201, 201, 201, 201, 201, 201, 105, 68, 68, 68, 68, 27, 27, 8, 1, 192, 192, 192, 192] 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: 720 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052406 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052406 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052406/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052406 Building REAL250005052407 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052407' /scratch/stefan/7921156/working/building/REAL250005052407 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052407 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052407/0 /scratch/stefan/7921156/working/building/REAL250005052407 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/542 `/scratch/stefan/7921156/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C)(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052407.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052407 none C=C1CC(C)(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 6, 6, 6, 32, 32, 103, 176, 176, 176, 188, 188, 188, 188, 188, 1, 1, 1, 1, 1, 2, 2, 2, 6, 32, 32, 32, 32, 103, 103, 176, 188, 1, 1] 188 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 23, 24, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 663 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: REAL250005052407 none C=C1CC(C)(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 102, 188, 102, 102, 76, 31, 75, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 188, 188, 188, 188, 102, 76, 76, 76, 76, 31, 31, 9, 1, 188, 188] 188 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: 641 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052407 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052407 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052407/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052407 Building REAL250005052408 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052408' /scratch/stefan/7921156/working/building/REAL250005052408 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052408 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052408/0 /scratch/stefan/7921156/working/building/REAL250005052408 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/543 `/scratch/stefan/7921156/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CF)CC1) `REAL250005052408.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052408 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 15, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 57, 99, 99, 99, 190, 201, 190, 190, 57, 57, 57, 57, 18, 18, 6, 1, 99, 201, 201, 190, 190, 190, 190] 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: 693 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: REAL250005052408 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 15, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 7, 28, 96, 186, 186, 186, 190, 190, 190, 190, 190, 7, 1, 7, 1, 1, 10, 1, 1, 28, 28, 28, 28, 96, 96, 186, 190, 7, 10, 10, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 13, 15, 16, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 667 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052408 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052408 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052408/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052408 Building REAL250005052409 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052409' /scratch/stefan/7921156/working/building/REAL250005052409 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052409 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052409/0 /scratch/stefan/7921156/working/building/REAL250005052409 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/544 `/scratch/stefan/7921156/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC2(CC2)C1) `REAL250005052409.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052409 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC2(CC2)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 78, 117, 117, 117, 201, 201, 201, 201, 201, 78, 78, 78, 78, 28, 28, 9, 1, 117, 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]) total number of confs: 706 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: REAL250005052409 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC2(CC2)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 12, 45, 128, 194, 194, 194, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 128, 128, 194, 201, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 723 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052409 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052409 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052409/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052409 Building REAL250005052410 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052410' /scratch/stefan/7921156/working/building/REAL250005052410 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052410 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052410/0 /scratch/stefan/7921156/working/building/REAL250005052410 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/545 `/scratch/stefan/7921156/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052410.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052410 none CCCCCCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 197, 182, 167, 137, 58, 58, 58, 38, 15, 38, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 181, 181, 169, 169, 137, 137, 58, 38, 38, 38, 38, 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: 908 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052410 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052410 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052410/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052410 Building REAL250005052411 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052411' /scratch/stefan/7921156/working/building/REAL250005052411 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052411 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052411/0 /scratch/stefan/7921156/working/building/REAL250005052411 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/546 `/scratch/stefan/7921156/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052411.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052411 none CC(C)C(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 190, 194, 119, 190, 119, 119, 76, 28, 74, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 194, 194, 190, 190, 190, 190, 119, 76, 76, 76, 76, 28, 28, 9, 1] 194 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: 820 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052411 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052411 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052411/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052411 Building REAL250005052412 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052412' /scratch/stefan/7921156/working/building/REAL250005052412 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052412 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052412/0 /scratch/stefan/7921156/working/building/REAL250005052412 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/547 `/scratch/stefan/7921156/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(C)C1) `REAL250005052412.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052412 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 75, 117, 117, 117, 201, 201, 201, 201, 201, 75, 75, 75, 75, 26, 26, 8, 1, 117, 201, 201, 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: 689 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: REAL250005052412 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 10, 39, 129, 195, 195, 195, 201, 201, 201, 201, 201, 10, 1, 10, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 129, 129, 195, 201, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 39, 40, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38]) total number of confs: 744 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052412 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052412 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052412/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052412 Building REAL250005052413 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052413' /scratch/stefan/7921156/working/building/REAL250005052413 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052413 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052413/0 /scratch/stefan/7921156/working/building/REAL250005052413 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/548 `/scratch/stefan/7921156/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052413.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052413 none C#CCOCCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 152, 131, 131, 51, 51, 51, 33, 21, 33, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 131, 131, 131, 131, 51, 33, 33, 33, 33, 21, 21, 5, 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: 825 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052413 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052413 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052413/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052413 Building REAL250005052414 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052414' /scratch/stefan/7921156/working/building/REAL250005052414 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052414 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052414/0 /scratch/stefan/7921156/working/building/REAL250005052414 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/549 `/scratch/stefan/7921156/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052414.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052414 none C#CCOC(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 155, 131, 79, 131, 79, 79, 47, 15, 46, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 131, 131, 131, 131, 79, 47, 47, 47, 47, 15, 15, 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: 863 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052414 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052414 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052414/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052414 Building REAL250005052415 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052415' /scratch/stefan/7921156/working/building/REAL250005052415 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052415 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052415/0 /scratch/stefan/7921156/working/building/REAL250005052415 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/550 `/scratch/stefan/7921156/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)C(N)=O) `REAL250005052415.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052415 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [64, 27, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 65, 113, 113, 113, 168, 168, 168, 195, 195, 65, 65, 65, 65, 27, 27, 10, 1, 113, 168, 168, 168, 168, 168, 168, 195, 195] 195 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: 776 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052415 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052415 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052415/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052415 Building REAL250005052416 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052416' /scratch/stefan/7921156/working/building/REAL250005052416 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052416 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052416/0 /scratch/stefan/7921156/working/building/REAL250005052416 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/551 `/scratch/stefan/7921156/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)NC(=O)C1(C2CC2)CC1) `REAL250005052416.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052416 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C2CC2)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 27, 73, 150, 201, 201, 201, 201, 201, 201, 201, 201, 27, 10, 27, 1, 1, 1, 1, 10, 10, 73, 73, 73, 73, 150, 150, 201, 201, 27, 1, 1, 1, 1, 1, 10, 10, 10, 10] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 820 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052416 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C2CC2)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 76, 76, 76, 134, 201, 201, 134, 134, 45, 45, 45, 45, 17, 17, 4, 1, 76, 201, 201, 201, 201, 201, 134, 134, 134, 134] 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: 693 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: REAL250005052416 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C2CC2)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 7, 22, 64, 125, 125, 125, 134, 134, 134, 134, 134, 7, 1, 7, 1, 1, 10, 10, 1, 1, 22, 22, 22, 22, 64, 64, 125, 134, 7, 10, 10, 10, 10, 10, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 13, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 470 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052416 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052416 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052416/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052416 Building REAL250005052417 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052417' /scratch/stefan/7921156/working/building/REAL250005052417 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052417 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052417/0 /scratch/stefan/7921156/working/building/REAL250005052417 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/552 `/scratch/stefan/7921156/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052417.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052417 none COC1CC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 11, 11, 11, 42, 42, 119, 198, 198, 198, 201, 201, 201, 201, 201, 1, 6, 6, 6, 1, 1, 1, 1, 11, 42, 42, 42, 42, 119, 119, 198, 201, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 20, 24, 25, 26, 27, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052417 none COC1CC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 110, 110, 110, 64, 20, 62, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 110, 64, 64, 64, 64, 20, 20, 6, 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: 693 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052417 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052417 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052417/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052417 Building REAL250005052418 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052418' /scratch/stefan/7921156/working/building/REAL250005052418 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052418 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052418/0 /scratch/stefan/7921156/working/building/REAL250005052418 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/553 `/scratch/stefan/7921156/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)NC(=O)[C@H]1C[C@H]1C(N)=O) `REAL250005052418.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052418 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1C[C@H]1C(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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [46, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 47, 70, 70, 70, 85, 85, 85, 85, 85, 95, 95, 47, 47, 47, 47, 21, 21, 9, 1, 70, 85, 85, 95, 95] 95 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: 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: REAL250005052418 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1C[C@H]1C(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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [22, 9, 22, 56, 76, 76, 76, 85, 85, 85, 85, 85, 9, 1, 9, 1, 1, 1, 1, 1, 1, 8, 8, 22, 22, 22, 22, 56, 56, 76, 85, 9, 1, 1, 8, 8] 95 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052418 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052418 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052418/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052418 Building REAL250005052419 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052419' /scratch/stefan/7921156/working/building/REAL250005052419 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052419 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052419/0 /scratch/stefan/7921156/working/building/REAL250005052419 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/554 `/scratch/stefan/7921156/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005052419.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052419 none CC[C@@H](C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 15, 15, 15, 15, 15, 9, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 16, 16, 16, 16, 16, 15, 15, 15, 15, 15, 9, 9, 4, 1, 15, 15, 15, 15, 15, 15] 16 rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 69 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052419 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052419 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052419/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052419 Building REAL250005052420 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052420' /scratch/stefan/7921156/working/building/REAL250005052420 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052420 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052420/0 /scratch/stefan/7921156/working/building/REAL250005052420 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/555 `/scratch/stefan/7921156/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CF)CCC1) `REAL250005052420.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052420 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CF)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.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [52, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 53, 99, 99, 99, 196, 201, 196, 196, 196, 53, 53, 53, 53, 18, 18, 6, 1, 99, 201, 201, 196, 196, 196, 196, 196, 196] 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: 677 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052420 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CF)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.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 25, 87, 183, 183, 183, 196, 196, 196, 196, 196, 6, 1, 6, 1, 1, 10, 1, 1, 1, 25, 25, 25, 25, 87, 87, 183, 196, 6, 10, 10, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 665 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052420 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052420 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052420/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052420 Building REAL250005052421 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052421' /scratch/stefan/7921156/working/building/REAL250005052421 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052421 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052421/0 /scratch/stefan/7921156/working/building/REAL250005052421 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/556 `/scratch/stefan/7921156/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H]1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052421.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052421 none CC[C@@H]1C[C@H]1C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 42, 42, 100, 159, 159, 159, 169, 169, 169, 169, 169, 3, 3, 3, 3, 3, 1, 1, 13, 42, 42, 42, 42, 100, 100, 159, 169] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 610 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: REAL250005052421 none CC[C@@H]1C[C@H]1C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 169, 169, 169, 169, 79, 169, 79, 79, 50, 18, 50, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 169, 169, 79, 50, 50, 50, 50, 18, 18, 4, 1] 201 rigid atoms, others: [37, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 741 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052421 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052421 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052421/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052421 Building REAL250005052422 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052422' /scratch/stefan/7921156/working/building/REAL250005052422 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052422 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052422/0 /scratch/stefan/7921156/working/building/REAL250005052422 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/557 `/scratch/stefan/7921156/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052422.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052422 none CC(C)CCCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 196, 167, 151, 149, 50, 50, 50, 31, 12, 31, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 196, 201, 201, 201, 201, 196, 193, 186, 186, 149, 149, 50, 31, 31, 31, 31, 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: 1356 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052422 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052422 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052422/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052422 Building REAL250005052423 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052423' /scratch/stefan/7921156/working/building/REAL250005052423 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052423 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052423/0 /scratch/stefan/7921156/working/building/REAL250005052423 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/558 `/scratch/stefan/7921156/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=N1) `REAL250005052423.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052423 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 1, 8, 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, 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] 0 hydrogens 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, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 59, 87, 87, 87, 165, 201, 201, 201, 201, 59, 59, 59, 59, 25, 25, 8, 1, 87, 165, 165, 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: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052423 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 1, 8, 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, 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] 0 hydrogens 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, 47, 88, 163, 196, 196, 196, 201, 201, 201, 201, 201, 47, 9, 47, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 163, 163, 196, 201, 47, 9, 9, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 798 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052423 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052423 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052423/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052423 Building REAL250005052424 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052424' /scratch/stefan/7921156/working/building/REAL250005052424 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052424 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052424/0 /scratch/stefan/7921156/working/building/REAL250005052424 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/559 `/scratch/stefan/7921156/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)NC(=O)CCNC(N)=O) `REAL250005052424.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052424 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCNC(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.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [38, 18, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 38, 55, 55, 55, 93, 98, 109, 109, 109, 38, 38, 38, 38, 18, 18, 6, 1, 55, 93, 93, 98, 98, 109, 109, 109] 109 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: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052424 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052424 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052424/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052424 Building REAL250005052425 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052425' /scratch/stefan/7921156/working/building/REAL250005052425 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052425 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052425/0 /scratch/stefan/7921156/working/building/REAL250005052425 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/560 `/scratch/stefan/7921156/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)NC(=O)C1=NSC=C1) `REAL250005052425.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052425 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NSC=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.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [76, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 76, 102, 102, 102, 104, 104, 104, 104, 76, 76, 76, 76, 33, 33, 9, 1, 102, 104, 104] 104 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]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052425 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NSC=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.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [17, 5, 17, 51, 99, 99, 99, 104, 104, 104, 104, 104, 5, 1, 5, 1, 1, 1, 1, 1, 17, 17, 17, 17, 51, 51, 99, 104, 5, 1, 1] 104 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052425 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052425 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052425/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052425 Building REAL250005052426 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052426' /scratch/stefan/7921156/working/building/REAL250005052426 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052426 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052426/0 /scratch/stefan/7921156/working/building/REAL250005052426 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/561 `/scratch/stefan/7921156/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)NC(=O)C(C)C1CCC1) `REAL250005052426.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052426 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 72, 118, 118, 118, 200, 200, 201, 201, 201, 72, 72, 72, 72, 25, 25, 8, 1, 118, 200, 200, 200, 200, 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: 830 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052426 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 22, 67, 151, 196, 196, 196, 201, 201, 201, 201, 201, 22, 5, 22, 1, 5, 1, 1, 1, 1, 67, 67, 67, 67, 151, 151, 196, 201, 22, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 15, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 769 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052426 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052426 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052426/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052426 Building REAL250005052427 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052427' /scratch/stefan/7921156/working/building/REAL250005052427 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052427 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052427/0 /scratch/stefan/7921156/working/building/REAL250005052427 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/562 `/scratch/stefan/7921156/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)NC(=O)C1COC(C)C1) `REAL250005052427.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052427 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [74, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 76, 116, 116, 116, 177, 177, 177, 177, 177, 76, 76, 76, 76, 30, 30, 11, 1, 116, 177, 177, 177, 177, 177, 177, 177, 177, 177] 177 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: 626 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: REAL250005052427 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 10, 33, 101, 167, 167, 167, 177, 177, 177, 177, 177, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 101, 101, 167, 177, 10, 1, 1, 1, 1, 2, 2, 2, 1, 1] 177 rigid atoms, others: [32, 33, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 626 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052427 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052427 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052427/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052427 Building REAL250005052428 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052428' /scratch/stefan/7921156/working/building/REAL250005052428 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052428 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052428/0 /scratch/stefan/7921156/working/building/REAL250005052428 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/563 `/scratch/stefan/7921156/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC12CC2) `REAL250005052428.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052428 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [67, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 70, 108, 108, 108, 201, 201, 201, 201, 70, 70, 70, 70, 26, 26, 8, 1, 108, 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]) total number of confs: 700 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: REAL250005052428 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [52, 13, 52, 137, 195, 195, 195, 201, 201, 201, 201, 201, 13, 1, 13, 1, 1, 1, 1, 1, 52, 52, 52, 52, 137, 137, 195, 201, 13, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 753 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052428 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052428 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052428/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052428 Building REAL250005052429 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052429' /scratch/stefan/7921156/working/building/REAL250005052429 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052429 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052429/0 /scratch/stefan/7921156/working/building/REAL250005052429 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/564 `/scratch/stefan/7921156/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CNC=N1) `REAL250005052429.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052429 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', '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, 1, 11, 5, 1, 1, 8, 1, 8, 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, 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] 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: [40, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 40, 56, 56, 56, 99, 115, 115, 115, 115, 40, 40, 40, 40, 19, 19, 7, 1, 56, 99, 99, 115, 115, 115] 115 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: 428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052429 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', '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, 1, 11, 5, 1, 1, 8, 1, 8, 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, 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] 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: [53, 31, 53, 85, 110, 110, 110, 115, 115, 115, 115, 115, 31, 9, 31, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 85, 85, 110, 115, 31, 9, 9, 1, 1, 1] 115 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 456 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052429 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052429/1 /scratch/stefan/7921156/working/building/REAL250005052429 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/565 `/scratch/stefan/7921156/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CN=CN1) `REAL250005052429.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052429/1/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: REAL250005052429 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 51, 77, 77, 77, 168, 201, 201, 201, 201, 51, 51, 51, 51, 23, 23, 9, 1, 77, 168, 168, 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: 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: REAL250005052429 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 31, 69, 134, 191, 191, 191, 201, 201, 201, 201, 201, 31, 5, 31, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 134, 134, 191, 201, 31, 5, 5, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 771 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052429 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052429 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052429/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052429/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052429 Building REAL250005052430 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052430' /scratch/stefan/7921156/working/building/REAL250005052430 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052430 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052430/0 /scratch/stefan/7921156/working/building/REAL250005052430 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/566 `/scratch/stefan/7921156/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052430.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052430 none C=CCC(C)(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 65, 131, 131, 65, 65, 39, 14, 39, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 131, 131, 131, 131, 131, 131, 65, 39, 39, 39, 39, 14, 14, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 912 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052430 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052430 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052430/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052430 Building REAL250005052431 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052431' /scratch/stefan/7921156/working/building/REAL250005052431 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052431 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052431/0 /scratch/stefan/7921156/working/building/REAL250005052431 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/567 `/scratch/stefan/7921156/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC12CCC2) `REAL250005052431.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052431 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 27, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 76, 117, 117, 117, 201, 201, 201, 201, 201, 76, 76, 76, 76, 27, 27, 8, 1, 117, 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]) total number of confs: 703 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052431 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 11, 48, 133, 192, 192, 192, 201, 201, 201, 201, 201, 11, 1, 11, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 133, 133, 192, 201, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 743 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052431 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052431 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052431/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052431 Building REAL250005052432 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052432' /scratch/stefan/7921156/working/building/REAL250005052432 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052432 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052432/0 /scratch/stefan/7921156/working/building/REAL250005052432 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/568 `/scratch/stefan/7921156/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CNC=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052432.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052432 none CC1=CNC=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 32, 32, 78, 123, 123, 123, 127, 127, 127, 127, 127, 2, 2, 2, 1, 1, 1, 11, 32, 32, 32, 32, 78, 78, 123, 127] 127 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 460 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052432 none CC1=CNC=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 127, 96, 96, 96, 62, 22, 61, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 127, 96, 62, 62, 62, 62, 22, 22, 9, 1] 127 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: 402 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052432 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052432 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052432/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052432 Building REAL250005052433 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052433' /scratch/stefan/7921156/working/building/REAL250005052433 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052433 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052433/0 /scratch/stefan/7921156/working/building/REAL250005052433 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/569 `/scratch/stefan/7921156/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)NC(=O)C1=NN(C)C=C1) `REAL250005052433.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052433 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN(C)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.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 8, 5, 1, 1, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [64, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 65, 92, 92, 92, 94, 94, 94, 94, 94, 65, 65, 65, 65, 26, 26, 8, 1, 92, 94, 94, 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: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052433 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN(C)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.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 8, 5, 1, 1, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 53, 87, 87, 87, 94, 94, 94, 94, 94, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 53, 53, 87, 94, 6, 2, 2, 2, 1, 1] 94 rigid atoms, others: [33, 34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052433 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052433 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052433/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052433 Building REAL250005052434 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052434' /scratch/stefan/7921156/working/building/REAL250005052434 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052434 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052434/0 /scratch/stefan/7921156/working/building/REAL250005052434 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/570 `/scratch/stefan/7921156/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(F)CCCC1) `REAL250005052434.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052434 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(F)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.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [67, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 102, 102, 102, 150, 150, 150, 150, 150, 69, 69, 69, 69, 23, 23, 9, 1, 102, 150, 150, 150, 150, 150, 150, 150, 150] 150 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: 542 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052434 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(F)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.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 9, 39, 100, 146, 146, 146, 150, 150, 150, 150, 150, 9, 1, 9, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 100, 100, 146, 150, 9, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 552 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052434 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052434 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052434/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052434 Building REAL250005052435 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052435' /scratch/stefan/7921156/working/building/REAL250005052435 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052435 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052435/0 /scratch/stefan/7921156/working/building/REAL250005052435 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/571 `/scratch/stefan/7921156/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)NC(=O)C1=CN=CN1C) `REAL250005052435.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052435 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 8, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [72, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 73, 105, 105, 105, 115, 115, 115, 115, 115, 73, 73, 73, 73, 32, 32, 9, 1, 105, 115, 115, 115, 115, 115] 115 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: 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: REAL250005052435 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 8, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [26, 10, 26, 67, 110, 110, 110, 115, 115, 115, 115, 115, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 67, 67, 110, 115, 10, 1, 1, 2, 2, 2] 115 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 410 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052435 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052435 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052435/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052435 Building REAL250005052436 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052436' /scratch/stefan/7921156/working/building/REAL250005052436 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052436 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052436/0 /scratch/stefan/7921156/working/building/REAL250005052436 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/572 `/scratch/stefan/7921156/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)NC(=O)CC(=O)N(C)C) `REAL250005052436.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052436 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(=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.2', 'O.2', 'C.3', '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, 1, 11, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 14, 14, 14, 19, 23, 23, 23, 23, 10, 10, 10, 10, 6, 6, 3, 1, 14, 19, 19, 23, 23, 23, 23, 23, 23] 23 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052436 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052436 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052436/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052436 Building REAL250005052437 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052437' /scratch/stefan/7921156/working/building/REAL250005052437 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052437 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052437/0 /scratch/stefan/7921156/working/building/REAL250005052437 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/573 `/scratch/stefan/7921156/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)NC(=O)[C@@H]1C[C@H]1C1CC1) `REAL250005052437.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052437 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [104, 50, 104, 165, 201, 201, 201, 201, 201, 201, 201, 201, 50, 7, 50, 7, 7, 7, 1, 7, 1, 1, 1, 104, 104, 104, 104, 165, 165, 201, 201, 50, 7, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 793 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052437 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [46, 19, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 46, 69, 69, 69, 175, 175, 175, 175, 175, 201, 201, 46, 46, 46, 46, 18, 18, 3, 1, 69, 175, 175, 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]) total number of confs: 656 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052437 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [40, 12, 40, 101, 172, 172, 172, 175, 175, 175, 175, 175, 12, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 40, 101, 101, 172, 175, 12, 1, 1, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 651 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052437 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052437 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052437/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052437 Building REAL250005052438 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052438' /scratch/stefan/7921156/working/building/REAL250005052438 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052438 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052438/0 /scratch/stefan/7921156/working/building/REAL250005052438 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/574 `/scratch/stefan/7921156/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052438.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052438 none COCCC(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 113, 35, 113, 35, 35, 31, 11, 31, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 170, 170, 113, 113, 113, 113, 35, 31, 31, 31, 31, 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: 938 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052438 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052438 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052438/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052438 Building REAL250005052439 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052439' /scratch/stefan/7921156/working/building/REAL250005052439 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052439 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052439/0 /scratch/stefan/7921156/working/building/REAL250005052439 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/575 `/scratch/stefan/7921156/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CC)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052439.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052439 none CCC(C)(CC)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [139, 142, 91, 142, 142, 150, 91, 91, 63, 28, 61, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 142, 142, 142, 157, 157, 157, 157, 157, 91, 63, 63, 63, 63, 28, 28, 9, 1] 162 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: 909 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052439 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052439 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052439/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052439 Building REAL250005052440 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052440' /scratch/stefan/7921156/working/building/REAL250005052440 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052440 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052440/0 /scratch/stefan/7921156/working/building/REAL250005052440 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/576 `/scratch/stefan/7921156/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005052440.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052440 none COCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 9, 1, 1, 1, 6, 6, 6, 22, 22, 58, 136, 136, 136, 139, 139, 139, 139, 139, 1, 1, 25, 25, 25, 9, 9, 6, 22, 22, 22, 22, 58, 58, 136, 139, 1, 1, 1, 1] 201 rigid atoms, others: [35, 2, 3, 4, 37, 38, 19, 20, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052440 none COCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 139, 72, 72, 72, 39, 17, 39, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 139, 139, 201, 201, 201, 201, 201, 72, 39, 39, 39, 39, 17, 17, 4, 1, 139, 139, 139, 139] 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: 785 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052440 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052440 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052440/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052440 Building REAL250005052441 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052441' /scratch/stefan/7921156/working/building/REAL250005052441 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052441 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052441/0 /scratch/stefan/7921156/working/building/REAL250005052441 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/577 `/scratch/stefan/7921156/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052441.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052441 none COCC(C)(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 103, 65, 103, 103, 65, 65, 35, 15, 35, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 162, 103, 103, 103, 103, 103, 103, 65, 35, 35, 35, 35, 15, 15, 4, 1] 162 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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/7921156/working/building/REAL250005052441 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052441 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052441/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052441 Building REAL250005052442 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052442' /scratch/stefan/7921156/working/building/REAL250005052442 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052442 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052442/0 /scratch/stefan/7921156/working/building/REAL250005052442 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/578 `/scratch/stefan/7921156/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)NC(=O)[C@H]1CCCO1) `REAL250005052442.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052442 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [64, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 66, 99, 99, 99, 115, 115, 115, 115, 115, 66, 66, 66, 66, 25, 25, 8, 1, 99, 115, 115, 115, 115, 115, 115] 115 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: 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: REAL250005052442 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [29, 10, 29, 75, 113, 113, 113, 115, 115, 115, 115, 115, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 75, 75, 113, 115, 10, 1, 1, 1, 1, 1, 1] 115 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 417 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052442 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052442 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052442/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052442 Building REAL250005052443 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052443' /scratch/stefan/7921156/working/building/REAL250005052443 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052443 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052443/0 /scratch/stefan/7921156/working/building/REAL250005052443 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/579 `/scratch/stefan/7921156/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC(F)F) `REAL250005052443.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052443 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 28, 41, 41, 41, 141, 167, 201, 201, 28, 28, 28, 28, 11, 11, 4, 1, 41, 141, 141, 188, 188, 190] 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]) total number of confs: 959 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052443 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052443 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052443/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052443 Building REAL250005052444 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052444' /scratch/stefan/7921156/working/building/REAL250005052444 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052444 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052444/0 /scratch/stefan/7921156/working/building/REAL250005052444 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/580 `/scratch/stefan/7921156/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)NC(=O)C1=CC(F)=CN1) `REAL250005052444.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052444 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(F)=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 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: [53, 22, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 53, 85, 85, 85, 94, 94, 94, 94, 94, 53, 53, 53, 53, 22, 22, 10, 1, 85, 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]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052444 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(F)=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 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: [20, 6, 20, 58, 89, 89, 89, 94, 94, 94, 94, 94, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 58, 58, 89, 94, 6, 1, 1, 1] 94 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 348 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052444 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052444 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052444/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052444 Building REAL250005052445 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052445' /scratch/stefan/7921156/working/building/REAL250005052445 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052445 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052445/0 /scratch/stefan/7921156/working/building/REAL250005052445 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/581 `/scratch/stefan/7921156/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)NC(=O)CC1(C)CC1) `REAL250005052445.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052445 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 59, 92, 92, 92, 181, 201, 201, 201, 59, 59, 59, 59, 22, 22, 5, 1, 92, 181, 181, 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: 820 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052445 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 26, 75, 154, 201, 201, 201, 201, 201, 201, 201, 201, 26, 8, 26, 1, 1, 1, 1, 1, 75, 75, 75, 75, 154, 154, 201, 201, 26, 8, 8, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 807 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052445 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052445 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052445/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052445 Building REAL250005052446 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052446' /scratch/stefan/7921156/working/building/REAL250005052446 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052446 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052446/0 /scratch/stefan/7921156/working/building/REAL250005052446 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/582 `/scratch/stefan/7921156/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CCF)CC1) `REAL250005052446.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052446 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CCF)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [39, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 70, 70, 70, 143, 201, 201, 143, 143, 39, 39, 39, 39, 14, 14, 4, 1, 70, 201, 201, 201, 201, 143, 143, 143, 143] 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: 786 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: REAL250005052446 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CCF)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 7, 25, 68, 134, 134, 134, 143, 143, 143, 143, 143, 7, 1, 7, 1, 1, 7, 16, 1, 1, 25, 25, 25, 25, 68, 68, 134, 143, 7, 7, 7, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 13, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 541 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052446 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052446 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052446/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052446 Building REAL250005052447 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052447' /scratch/stefan/7921156/working/building/REAL250005052447 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052447 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052447/0 /scratch/stefan/7921156/working/building/REAL250005052447 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/583 `/scratch/stefan/7921156/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1COC2) `REAL250005052447.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052447 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1COC2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 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, 7, 3, 7, 3, 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] 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: [72, 29, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 73, 101, 101, 101, 161, 161, 161, 161, 161, 161, 73, 73, 73, 73, 29, 29, 8, 1, 101, 161, 161, 161, 161, 161, 161] 161 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]) total number of confs: 464 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: REAL250005052447 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1COC2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 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, 7, 3, 7, 3, 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] 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: [27, 6, 27, 93, 151, 152, 151, 161, 161, 161, 161, 161, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 93, 93, 152, 161, 6, 1, 1, 1, 1, 1, 1] 161 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 572 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052447 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052447 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052447/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052447 Building REAL250005052448 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052448' /scratch/stefan/7921156/working/building/REAL250005052448 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052448 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052448/0 /scratch/stefan/7921156/working/building/REAL250005052448 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/584 `/scratch/stefan/7921156/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)NC(=O)C1(C)CC1) `REAL250005052448.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052448 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [60, 28, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 61, 83, 83, 83, 157, 157, 157, 61, 61, 61, 61, 28, 28, 11, 1, 83, 157, 157, 157, 157, 157, 157, 157] 157 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: 552 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: REAL250005052448 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [31, 7, 31, 91, 149, 149, 149, 157, 157, 157, 157, 157, 7, 1, 7, 1, 1, 1, 1, 31, 31, 31, 31, 91, 91, 149, 157, 7, 2, 2, 2, 1, 1, 1, 1] 157 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 556 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052448 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052448 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052448/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052448 Building REAL250005052449 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052449' /scratch/stefan/7921156/working/building/REAL250005052449 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052449 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052449/0 /scratch/stefan/7921156/working/building/REAL250005052449 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/585 `/scratch/stefan/7921156/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)NC(=O)C1=CNC=C1) `REAL250005052449.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052449 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNC=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.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [68, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 68, 102, 102, 102, 153, 153, 153, 153, 68, 68, 68, 68, 28, 28, 9, 1, 102, 153, 153, 153, 153] 153 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]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052449 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNC=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.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [22, 5, 22, 89, 146, 146, 146, 153, 153, 153, 153, 153, 5, 1, 5, 1, 1, 1, 1, 1, 22, 22, 22, 22, 89, 89, 146, 153, 5, 1, 1, 1, 1] 153 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 539 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052449 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052449 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052449/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052449 Building REAL250005052450 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052450' /scratch/stefan/7921156/working/building/REAL250005052450 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052450 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052450/0 /scratch/stefan/7921156/working/building/REAL250005052450 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/586 `/scratch/stefan/7921156/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(C)C1CC1) `REAL250005052450.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052450 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 42, 62, 62, 62, 166, 199, 201, 201, 201, 42, 42, 42, 42, 17, 17, 4, 1, 62, 166, 166, 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: 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: REAL250005052450 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 45, 95, 151, 201, 201, 201, 201, 201, 201, 201, 201, 45, 15, 45, 3, 1, 3, 1, 1, 1, 95, 95, 95, 95, 151, 151, 201, 201, 45, 15, 15, 3, 4, 4, 4, 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: 821 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052450 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052450 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052450/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052450 Building REAL250005052451 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052451' /scratch/stefan/7921156/working/building/REAL250005052451 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052451 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052451/0 /scratch/stefan/7921156/working/building/REAL250005052451 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/587 `/scratch/stefan/7921156/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)NC(=O)C1=CSN=N1) `REAL250005052451.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052451 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSN=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.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 14, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [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] 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: [79, 35, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 80, 106, 106, 106, 111, 111, 111, 111, 80, 80, 80, 80, 35, 35, 9, 1, 106, 111] 111 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]) total number of confs: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052451 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSN=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.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 14, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [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] 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: [21, 7, 21, 62, 104, 104, 104, 111, 111, 111, 111, 111, 7, 1, 7, 1, 1, 1, 1, 1, 21, 21, 21, 21, 62, 62, 104, 111, 7, 1] 111 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 387 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052451 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052451 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052451/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052451 Building REAL250005052452 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052452' /scratch/stefan/7921156/working/building/REAL250005052452 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052452 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052452/0 /scratch/stefan/7921156/working/building/REAL250005052452 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/588 `/scratch/stefan/7921156/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)NC(=O)C1(C)CCCC1) `REAL250005052452.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052452 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 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: [67, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 104, 104, 104, 163, 163, 163, 163, 163, 69, 69, 69, 69, 29, 29, 9, 1, 104, 163, 163, 163, 163, 163, 163, 163, 163, 163, 163, 163] 163 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: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052452 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 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: [22, 5, 22, 86, 155, 155, 155, 163, 163, 163, 163, 163, 5, 1, 5, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 86, 86, 155, 163, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 163 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 574 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052452 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052452 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052452/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052452 Building REAL250005052453 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052453' /scratch/stefan/7921156/working/building/REAL250005052453 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052453 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052453/0 /scratch/stefan/7921156/working/building/REAL250005052453 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/589 `/scratch/stefan/7921156/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CO1) `REAL250005052453.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052453 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [56, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 57, 75, 75, 75, 81, 81, 81, 81, 57, 57, 57, 57, 24, 24, 9, 1, 75, 81, 81] 81 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]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052453 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 18, 45, 77, 77, 77, 81, 81, 81, 81, 81, 7, 1, 7, 1, 1, 1, 1, 1, 18, 18, 18, 18, 45, 45, 77, 81, 7, 1, 1] 81 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052453 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052453 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052453/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052453 Building REAL250005052454 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052454' /scratch/stefan/7921156/working/building/REAL250005052454 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052454 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052454/0 /scratch/stefan/7921156/working/building/REAL250005052454 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/590 `/scratch/stefan/7921156/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052454.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052454 none CNC(=O)NCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 128, 128, 128, 107, 76, 76, 76, 45, 16, 45, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 128, 107, 107, 76, 45, 45, 45, 45, 16, 16, 4, 1] 142 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: 568 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052454 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052454 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052454/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052454 Building REAL250005052455 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052455' /scratch/stefan/7921156/working/building/REAL250005052455 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052455 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052455/0 /scratch/stefan/7921156/working/building/REAL250005052455 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/591 `/scratch/stefan/7921156/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052455.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052455 none C=CCCOCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 100, 70, 24, 24, 24, 12, 8, 12, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 131, 131, 70, 70, 24, 12, 12, 12, 12, 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: 858 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052455 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052455 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052455/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052455 Building REAL250005052456 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052456' /scratch/stefan/7921156/working/building/REAL250005052456 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052456 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052456/0 /scratch/stefan/7921156/working/building/REAL250005052456 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/592 `/scratch/stefan/7921156/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052456.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052456 none C=CCOC(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 127, 87, 55, 87, 55, 55, 36, 11, 36, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 87, 87, 87, 87, 55, 36, 36, 36, 36, 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: 815 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052456 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052456 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052456/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052456 Building REAL250005052457 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052457' /scratch/stefan/7921156/working/building/REAL250005052457 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052457 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052457/0 /scratch/stefan/7921156/working/building/REAL250005052457 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/593 `/scratch/stefan/7921156/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)NC(=O)CCCC(N)=O) `REAL250005052457.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052457 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [33, 18, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 33, 44, 44, 44, 102, 113, 180, 191, 191, 33, 33, 33, 33, 18, 18, 5, 1, 44, 102, 102, 133, 133, 170, 169, 191, 191] 191 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: 938 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052457 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052457 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052457/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052457 Building REAL250005052458 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052458' /scratch/stefan/7921156/working/building/REAL250005052458 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052458 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052458/0 /scratch/stefan/7921156/working/building/REAL250005052458 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/594 `/scratch/stefan/7921156/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052458.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052458 none CC1=NNC=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 24, 24, 55, 83, 83, 83, 88, 88, 88, 88, 88, 2, 2, 2, 1, 1, 9, 24, 24, 24, 24, 55, 55, 83, 88] 88 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 330 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: REAL250005052458 none CC1=NNC=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 88, 77, 77, 77, 57, 21, 56, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 88, 77, 57, 57, 57, 57, 21, 21, 9, 1] 88 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: 308 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052458 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052458 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052458/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052458 Building REAL250005052459 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052459' /scratch/stefan/7921156/working/building/REAL250005052459 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052459 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052459/0 /scratch/stefan/7921156/working/building/REAL250005052459 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/595 `/scratch/stefan/7921156/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)NN=N1) `REAL250005052459.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052459 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)NN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 11, 36, 36, 86, 118, 118, 118, 124, 124, 124, 124, 124, 1, 1, 1, 2, 2, 2, 11, 36, 36, 36, 36, 86, 86, 118, 124, 1] 124 rigid atoms, others: [0, 1, 2, 3, 33, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 453 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: REAL250005052459 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)NN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 77, 77, 77, 52, 24, 52, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 124, 77, 52, 52, 52, 52, 24, 24, 10, 1, 124] 124 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 364 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052459 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052459/1 /scratch/stefan/7921156/working/building/REAL250005052459 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/596 `/scratch/stefan/7921156/working/3D/596' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNN=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052459.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052459/1/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: REAL250005052459 none CC1=NNN=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 14, 14, 54, 99, 99, 99, 106, 106, 106, 106, 106, 2, 2, 2, 1, 3, 14, 14, 14, 14, 54, 54, 99, 106] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 373 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: REAL250005052459 none CC1=NNN=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 106, 106, 75, 31, 75, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 75, 75, 75, 75, 31, 31, 9, 1] 106 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: 393 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052459 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052459 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052459/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052459/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052459 Building REAL250005052460 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052460' /scratch/stefan/7921156/working/building/REAL250005052460 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052460 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052460/0 /scratch/stefan/7921156/working/building/REAL250005052460 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/597 `/scratch/stefan/7921156/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(OC)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052460.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052460 none CCCC(OC)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 116, 71, 116, 139, 71, 71, 43, 10, 41, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 196, 201, 198, 198, 116, 139, 139, 139, 71, 43, 43, 43, 43, 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: 986 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052460 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052460 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052460/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052460 Building REAL250005052461 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052461' /scratch/stefan/7921156/working/building/REAL250005052461 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052461 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052461/0 /scratch/stefan/7921156/working/building/REAL250005052461 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/598 `/scratch/stefan/7921156/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C(C)(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052461.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052461 none C=C(C)C(C)(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 201, 118, 200, 200, 118, 118, 67, 24, 65, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 200, 200, 200, 200, 118, 67, 67, 67, 67, 24, 24, 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: 824 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052461 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052461 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052461/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052461 Building REAL250005052462 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052462' /scratch/stefan/7921156/working/building/REAL250005052462 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052462 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052462/0 /scratch/stefan/7921156/working/building/REAL250005052462 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/599 `/scratch/stefan/7921156/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)CC(N)=O) `REAL250005052462.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052462 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 137, 137, 191, 201, 201, 32, 32, 32, 32, 13, 13, 4, 1, 50, 137, 137, 137, 137, 191, 191, 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: 867 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052462 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052462 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052462/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052462 Building REAL250005052463 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052463' /scratch/stefan/7921156/working/building/REAL250005052463 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052463 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052463/0 /scratch/stefan/7921156/working/building/REAL250005052463 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/600 `/scratch/stefan/7921156/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)NC(=O)C1CCNC1=O) `REAL250005052463.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052463 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCNC1=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [82, 35, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 84, 137, 137, 137, 175, 175, 175, 175, 175, 84, 84, 84, 84, 35, 35, 9, 1, 137, 175, 175, 175, 175, 175, 175] 175 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: 639 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052463 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCNC1=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [36, 11, 36, 118, 167, 167, 167, 175, 175, 175, 175, 175, 11, 1, 11, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 118, 118, 167, 175, 11, 1, 1, 1, 1, 1, 1] 175 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 651 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052463 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052463 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052463/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052463 Building REAL250005052464 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052464' /scratch/stefan/7921156/working/building/REAL250005052464 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052464 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052464/0 /scratch/stefan/7921156/working/building/REAL250005052464 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/601 `/scratch/stefan/7921156/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052464.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052464 none C=CC(C)(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 114, 200, 201, 114, 114, 62, 19, 61, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 200, 201, 201, 201, 201, 114, 62, 62, 62, 62, 19, 19, 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: 818 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052464 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052464 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052464/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052464 Building REAL250005052465 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052465' /scratch/stefan/7921156/working/building/REAL250005052465 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005052465 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052465/0 /scratch/stefan/7921156/working/building/REAL250005052465 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/602 `/scratch/stefan/7921156/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCC[N@@H+]1C) `REAL250005052465.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052465 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCC[N@@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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 22, 22, 22, 25, 25, 25, 25, 25, 25, 25, 18, 18, 18, 18, 12, 12, 8, 1, 22, 25, 25, 25, 25, 25, 25, 25, 25, 25] 25 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: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052465 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCC[N@@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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 20, 20, 20, 20, 25, 25, 25, 25, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 20, 20, 20, 25, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2] 25 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052465 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052465/1 /scratch/stefan/7921156/working/building/REAL250005052465 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/603 `/scratch/stefan/7921156/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCC[N@H+]1C) `REAL250005052465.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052465/1/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: REAL250005052465 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCC[N@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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 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]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052465 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCC[N@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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 6, 6, 6, 6, 7, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 7, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2] 7 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052465 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `2' /scratch/stefan/7921156/working/building/REAL250005052465/2 /scratch/stefan/7921156/working/building/REAL250005052465 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 2 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/604 `/scratch/stefan/7921156/working/3D/604' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCCN1C) `REAL250005052465.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005052465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052465/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052465 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 7, 5, 5, 5, 10, 5, 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, 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 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [76, 29, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 78, 114, 114, 114, 119, 119, 119, 119, 119, 119, 78, 78, 78, 78, 28, 28, 8, 1, 114, 119, 119, 119, 119, 119, 119, 119, 119, 119] 119 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]) 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: REAL250005052465 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 7, 5, 5, 5, 10, 5, 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, 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 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 20, 66, 114, 114, 114, 119, 119, 119, 119, 119, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 66, 66, 114, 119, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2] 119 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39]) total number of confs: 419 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052465 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052465 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052465/0.* 2: /scratch/stefan/7921156/working/building/REAL250005052465/2.* 1: /scratch/stefan/7921156/working/building/REAL250005052465/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052465 Building REAL250005052466 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052466' /scratch/stefan/7921156/working/building/REAL250005052466 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052466 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052466/0 /scratch/stefan/7921156/working/building/REAL250005052466 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/605 `/scratch/stefan/7921156/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1C) `REAL250005052466.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052466 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 29, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 80, 117, 117, 117, 201, 201, 201, 201, 201, 80, 80, 80, 80, 29, 29, 9, 1, 117, 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]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052466 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 12, 52, 135, 192, 192, 192, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 135, 135, 192, 201, 12, 1, 1, 2, 2, 2] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 742 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052466 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052466 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052466/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052466 Building REAL250005052467 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052467' /scratch/stefan/7921156/working/building/REAL250005052467 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052467 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052467/0 /scratch/stefan/7921156/working/building/REAL250005052467 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/606 `/scratch/stefan/7921156/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CCC1) `REAL250005052467.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052467 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [65, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 67, 96, 96, 96, 157, 157, 157, 157, 67, 67, 67, 67, 28, 28, 10, 1, 96, 157, 157, 157, 157, 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, 36, 37]) total number of confs: 561 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: REAL250005052467 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 5, 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, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [30, 6, 30, 95, 145, 145, 145, 157, 157, 157, 157, 157, 6, 1, 6, 1, 1, 1, 1, 1, 30, 30, 30, 30, 95, 95, 145, 157, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1] 157 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 549 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052467 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052467 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052467/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052467 Building REAL250005052468 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052468' /scratch/stefan/7921156/working/building/REAL250005052468 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052468 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052468/0 /scratch/stefan/7921156/working/building/REAL250005052468 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/607 `/scratch/stefan/7921156/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052468.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052468 none CCC(F)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 123, 180, 123, 123, 70, 23, 68, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 180, 123, 70, 70, 70, 70, 23, 23, 7, 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: 840 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052468 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052468 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052468/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052468 Building REAL250005052469 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052469' /scratch/stefan/7921156/working/building/REAL250005052469 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052469 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052469/0 /scratch/stefan/7921156/working/building/REAL250005052469 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/608 `/scratch/stefan/7921156/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)NC(=O)CCCF) `REAL250005052469.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052469 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 15, 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, 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] 0 hydrogens 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, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 36, 60, 60, 60, 169, 192, 201, 36, 36, 36, 36, 13, 13, 4, 1, 60, 169, 169, 200, 200, 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: 927 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052469 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052469 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052469/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052469 Building REAL250005052470 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052470' /scratch/stefan/7921156/working/building/REAL250005052470 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052470 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052470/0 /scratch/stefan/7921156/working/building/REAL250005052470 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/609 `/scratch/stefan/7921156/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052470.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052470 none CC1=COC=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 36, 36, 89, 125, 125, 125, 133, 133, 133, 133, 133, 2, 2, 2, 1, 1, 10, 36, 36, 36, 36, 89, 89, 125, 133] 133 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 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: REAL250005052470 none CC1=COC=C1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 133, 133, 87, 87, 87, 59, 23, 58, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 87, 59, 59, 59, 59, 23, 23, 10, 1] 133 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: 399 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052470 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052470 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052470/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052470 Building REAL250005052471 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052471' /scratch/stefan/7921156/working/building/REAL250005052471 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052471 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052471/0 /scratch/stefan/7921156/working/building/REAL250005052471 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/610 `/scratch/stefan/7921156/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)NC(=O)[C@H]1C[C@@H]1C) `REAL250005052471.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052471 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 80, 117, 117, 117, 201, 201, 201, 201, 201, 80, 80, 80, 80, 29, 29, 9, 1, 117, 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]) 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: REAL250005052471 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 12, 52, 135, 192, 192, 192, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 135, 135, 192, 201, 12, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052471 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052471 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052471/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052471 Building REAL250005052472 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052472' /scratch/stefan/7921156/working/building/REAL250005052472 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052472 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052472/0 /scratch/stefan/7921156/working/building/REAL250005052472 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/611 `/scratch/stefan/7921156/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)C=CCC1) `REAL250005052472.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052472 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)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.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 1, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [74, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 76, 109, 109, 109, 178, 178, 178, 178, 178, 76, 76, 76, 76, 34, 34, 10, 1, 109, 178, 178, 178, 178, 178, 178, 178, 178, 178] 178 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: 628 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: REAL250005052472 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)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.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 1, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [27, 6, 27, 96, 167, 167, 167, 178, 178, 178, 178, 178, 6, 1, 6, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 96, 96, 167, 178, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1] 178 rigid atoms, others: [33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 613 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052472 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052472 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052472/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052472 Building REAL250005052473 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052473' /scratch/stefan/7921156/working/building/REAL250005052473 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052473 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052473/0 /scratch/stefan/7921156/working/building/REAL250005052473 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/612 `/scratch/stefan/7921156/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)NC(=O)C1=NN(C)N=N1) `REAL250005052473.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052473 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN(C)N=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.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [62, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 62, 90, 90, 90, 122, 122, 122, 122, 122, 62, 62, 62, 62, 24, 24, 7, 1, 90, 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]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052473 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN(C)N=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.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [26, 6, 26, 72, 120, 120, 120, 122, 122, 122, 122, 122, 6, 1, 6, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 72, 72, 120, 122, 7, 2, 2, 2] 122 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 448 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052473 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052473 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052473/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052473 Building REAL250005052474 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052474' /scratch/stefan/7921156/working/building/REAL250005052474 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052474 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052474/0 /scratch/stefan/7921156/working/building/REAL250005052474 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/613 `/scratch/stefan/7921156/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)NC=N1) `REAL250005052474.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052474 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 11, 31, 31, 72, 110, 110, 110, 118, 118, 118, 118, 118, 1, 1, 1, 2, 2, 2, 11, 31, 31, 31, 31, 72, 72, 110, 118, 1, 1] 118 rigid atoms, others: [0, 1, 2, 3, 33, 34, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 429 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: REAL250005052474 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 77, 77, 77, 58, 26, 58, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 118, 118, 77, 58, 58, 58, 58, 26, 26, 10, 1, 118, 118] 118 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 365 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052474 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052474 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052474/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052474 Building REAL250005052475 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052475' /scratch/stefan/7921156/working/building/REAL250005052475 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052475 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052475/0 /scratch/stefan/7921156/working/building/REAL250005052475 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/614 `/scratch/stefan/7921156/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(F)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052475.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052475 none CC(C)C(F)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 122, 180, 122, 122, 70, 23, 68, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 180, 122, 70, 70, 70, 70, 23, 23, 6, 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: 844 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052475 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052475 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052475/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052475 Building REAL250005052476 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052476' /scratch/stefan/7921156/working/building/REAL250005052476 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052476 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052476/0 /scratch/stefan/7921156/working/building/REAL250005052476 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/615 `/scratch/stefan/7921156/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)C(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052476.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052476 none C=CC(C)C(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 139, 162, 88, 139, 88, 88, 59, 23, 59, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 162, 162, 162, 139, 139, 139, 139, 88, 59, 59, 59, 59, 23, 23, 6, 1] 162 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052476 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052476 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052476/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052476 Building REAL250005052477 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052477' /scratch/stefan/7921156/working/building/REAL250005052477 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052477 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052477/0 /scratch/stefan/7921156/working/building/REAL250005052477 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/616 `/scratch/stefan/7921156/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005052477.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052477 none CCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 6, 6, 6, 22, 22, 79, 142, 142, 142, 151, 151, 151, 151, 151, 1, 1, 1, 3, 3, 3, 3, 3, 6, 22, 22, 22, 22, 79, 79, 142, 151, 1, 1, 1, 1, 1, 1] 153 rigid atoms, others: [1, 2, 3, 36, 37, 35, 39, 40, 18, 19, 20, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 513 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: REAL250005052477 none CCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 151, 82, 82, 82, 56, 28, 55, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 151, 151, 151, 153, 153, 153, 153, 153, 82, 56, 56, 56, 56, 28, 28, 9, 1, 151, 151, 151, 151, 151, 151] 153 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: 546 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052477 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052477 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052477/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052477 Building REAL250005052478 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052478' /scratch/stefan/7921156/working/building/REAL250005052478 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052478 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052478/0 /scratch/stefan/7921156/working/building/REAL250005052478 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/617 `/scratch/stefan/7921156/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052478.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052478 none CC#CCCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 108, 30, 30, 30, 19, 9, 19, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 194, 187, 149, 149, 108, 108, 30, 19, 19, 19, 19, 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: 1017 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052478 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052478 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052478/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052478 Building REAL250005052479 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052479' /scratch/stefan/7921156/working/building/REAL250005052479 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052479 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052479/0 /scratch/stefan/7921156/working/building/REAL250005052479 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/618 `/scratch/stefan/7921156/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)NC(=O)[C@H]1[C@@H]2COC[C@@H]21) `REAL250005052479.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052479 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1[C@@H]2COC[C@@H]21 NO_LONG_NAME dock atom types: ['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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens 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, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 70, 109, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70, 70, 29, 29, 10, 1, 109, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 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, 30, 32, 33, 34, 35, 36]) total number of confs: 694 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052479 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1[C@@H]2COC[C@@H]21 NO_LONG_NAME dock atom types: ['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', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens 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, 12, 51, 131, 194, 194, 194, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 131, 131, 194, 201, 12, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 731 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052479 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052479 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052479/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052479 Building REAL250005052480 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052480' /scratch/stefan/7921156/working/building/REAL250005052480 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052480 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052480/0 /scratch/stefan/7921156/working/building/REAL250005052480 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/619 `/scratch/stefan/7921156/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)NC(=O)CCCC1CC1) `REAL250005052480.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052480 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 23, 29, 29, 29, 117, 117, 153, 201, 201, 23, 23, 23, 23, 9, 9, 3, 1, 29, 117, 117, 140, 140, 153, 153, 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: 979 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052480 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 55, 96, 167, 201, 201, 201, 201, 201, 201, 201, 201, 55, 11, 55, 7, 3, 1, 1, 1, 1, 96, 96, 96, 96, 167, 167, 201, 201, 55, 11, 11, 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: 861 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052480 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052480 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052480/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052480 Building REAL250005052481 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052481' /scratch/stefan/7921156/working/building/REAL250005052481 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052481 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052481/0 /scratch/stefan/7921156/working/building/REAL250005052481 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/620 `/scratch/stefan/7921156/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC1(C)C) `REAL250005052481.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052481 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC1(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 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: [54, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 54, 73, 73, 73, 81, 81, 81, 81, 81, 54, 54, 54, 54, 23, 23, 9, 1, 73, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81] 81 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: 300 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: REAL250005052481 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC1(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 18, 47, 77, 77, 77, 81, 81, 81, 81, 81, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 47, 47, 77, 81, 6, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 81 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40]) total number of confs: 305 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052481 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052481 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052481/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052481 Building REAL250005052482 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052482' /scratch/stefan/7921156/working/building/REAL250005052482 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052482 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052482/0 /scratch/stefan/7921156/working/building/REAL250005052482 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/621 `/scratch/stefan/7921156/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005052482.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052482 none CC1=COC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 58, 98, 98, 98, 107, 107, 107, 107, 107, 1, 2, 2, 2, 1, 6, 20, 20, 20, 20, 58, 58, 98, 107, 1] 107 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052482 none CC1=COC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 101, 101, 101, 76, 36, 76, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 101, 76, 76, 76, 76, 36, 36, 9, 1, 107] 107 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34]) total number of confs: 384 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052482 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052482 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052482/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052482 Building REAL250005052483 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052483' /scratch/stefan/7921156/working/building/REAL250005052483 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052483 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052483/0 /scratch/stefan/7921156/working/building/REAL250005052483 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/622 `/scratch/stefan/7921156/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(CC)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052483.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052483 none C=CC(CC)CC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 181, 109, 179, 201, 40, 40, 40, 33, 13, 33, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 194, 194, 194, 181, 200, 200, 201, 201, 201, 109, 109, 40, 33, 33, 33, 33, 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: 981 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052483 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052483 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052483/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052483 Building REAL250005052484 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052484' /scratch/stefan/7921156/working/building/REAL250005052484 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052484 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052484/0 /scratch/stefan/7921156/working/building/REAL250005052484 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/623 `/scratch/stefan/7921156/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)NC(=O)C(C)(C)C1CC1) `REAL250005052484.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052484 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 48, 80, 80, 80, 154, 154, 154, 201, 201, 48, 48, 48, 48, 18, 18, 4, 1, 80, 154, 154, 154, 154, 154, 154, 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: 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: REAL250005052484 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 30, 75, 158, 201, 201, 201, 201, 201, 201, 201, 201, 30, 11, 30, 1, 11, 11, 1, 1, 1, 75, 75, 75, 75, 158, 158, 201, 201, 30, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 811 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052484 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052484 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052484/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052484 Building REAL250005052485 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052485' /scratch/stefan/7921156/working/building/REAL250005052485 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052485 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052485/0 /scratch/stefan/7921156/working/building/REAL250005052485 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/624 `/scratch/stefan/7921156/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1C[C@H]2C[C@H]2C1) `REAL250005052485.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052485 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1C[C@H]2C[C@H]2C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 29, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 77, 123, 123, 123, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 77, 77, 29, 29, 8, 1, 123, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 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, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 702 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: REAL250005052485 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1C[C@H]2C[C@H]2C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 10, 42, 130, 196, 196, 196, 201, 201, 201, 201, 201, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 130, 130, 196, 201, 10, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 727 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052485 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052485 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052485/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052485 Building REAL250005052486 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052486' /scratch/stefan/7921156/working/building/REAL250005052486 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052486 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052486/0 /scratch/stefan/7921156/working/building/REAL250005052486 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/625 `/scratch/stefan/7921156/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)NC(=O)CC1=CON=C1) `REAL250005052486.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052486 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 12, 8, 1, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 38, 66, 66, 66, 98, 201, 201, 201, 201, 38, 38, 38, 38, 15, 15, 5, 1, 66, 98, 98, 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: 574 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052486 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 12, 8, 1, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 17, 56, 141, 199, 199, 199, 201, 201, 201, 201, 201, 17, 4, 17, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 141, 141, 199, 201, 17, 4, 4, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 780 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052486 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052486 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052486/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052486 Building REAL250005052487 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052487' /scratch/stefan/7921156/working/building/REAL250005052487 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052487 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052487/0 /scratch/stefan/7921156/working/building/REAL250005052487 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/626 `/scratch/stefan/7921156/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)C(C)(C)C) `REAL250005052487.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052487 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 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: [56, 25, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 58, 79, 79, 79, 91, 91, 91, 91, 91, 58, 58, 58, 58, 25, 25, 9, 1, 79, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91] 91 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: 373 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052487 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052487 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052487/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052487 Building REAL250005052488 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052488' /scratch/stefan/7921156/working/building/REAL250005052488 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052488 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052488/0 /scratch/stefan/7921156/working/building/REAL250005052488 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/627 `/scratch/stefan/7921156/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NNN=C1) `REAL250005052488.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052488 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [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] 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: [75, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 75, 87, 87, 87, 88, 88, 88, 88, 75, 75, 75, 75, 34, 34, 9, 1, 87, 88, 88] 88 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]) 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: REAL250005052488 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [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] 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: [16, 4, 16, 44, 82, 82, 82, 88, 88, 88, 88, 88, 4, 1, 4, 1, 1, 1, 1, 1, 16, 16, 16, 16, 44, 44, 82, 88, 4, 1, 1] 88 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052488 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052488/1 /scratch/stefan/7921156/working/building/REAL250005052488 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/628 `/scratch/stefan/7921156/working/3D/628' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=NN1) `REAL250005052488.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052488/1/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: REAL250005052488 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=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.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', '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, 1, 11, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [51, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 51, 65, 65, 65, 71, 71, 71, 71, 51, 51, 51, 51, 24, 24, 9, 1, 65, 71, 71] 71 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]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052488 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=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.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', '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, 1, 11, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 18, 45, 64, 64, 64, 71, 71, 71, 71, 71, 7, 1, 7, 1, 1, 1, 1, 1, 18, 18, 18, 18, 45, 45, 64, 71, 7, 1, 1] 71 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052488 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052488 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052488/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052488/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052488 Building REAL250005052489 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052489' /scratch/stefan/7921156/working/building/REAL250005052489 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052489 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052489/0 /scratch/stefan/7921156/working/building/REAL250005052489 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/629 `/scratch/stefan/7921156/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CC(N)=O) `REAL250005052489.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052489 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 6, 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: [34, 20, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 46, 46, 46, 64, 64, 71, 71, 34, 34, 34, 34, 20, 20, 10, 1, 46, 64, 64, 71, 71] 71 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]) total number of confs: 256 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052489 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052489 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052489/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052489 Building REAL250005052490 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052490' /scratch/stefan/7921156/working/building/REAL250005052490 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052490 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052490/0 /scratch/stefan/7921156/working/building/REAL250005052490 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/630 `/scratch/stefan/7921156/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)NC(=O)C1=NC(N)=NN1) `REAL250005052490.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052490 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC(N)=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.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 4, 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: [75, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 75, 116, 116, 116, 116, 116, 116, 116, 116, 75, 75, 75, 75, 33, 33, 10, 1, 116, 116, 116, 116] 116 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]) total number of confs: 427 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052490 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC(N)=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.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 4, 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: [14, 4, 14, 55, 107, 107, 107, 116, 116, 116, 116, 116, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 55, 55, 107, 116, 4, 1, 1, 1] 116 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 386 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052490 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052490 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052490/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052490 Building REAL250005052491 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052491' /scratch/stefan/7921156/working/building/REAL250005052491 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052491 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052491/0 /scratch/stefan/7921156/working/building/REAL250005052491 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/631 `/scratch/stefan/7921156/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052491.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052491 none COC(=O)CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 47, 67, 36, 36, 36, 25, 15, 25, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 67, 67, 67, 47, 47, 36, 25, 25, 25, 25, 15, 15, 4, 1] 67 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052491 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052491 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052491/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052491 Building REAL250005052492 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052492' /scratch/stefan/7921156/working/building/REAL250005052492 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052492 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052492/0 /scratch/stefan/7921156/working/building/REAL250005052492 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/632 `/scratch/stefan/7921156/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCSCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052492.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052492 none C#CCSCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 156, 106, 49, 49, 49, 29, 9, 29, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 106, 106, 49, 29, 29, 29, 29, 9, 9, 3, 1] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 769 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052492 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052492 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052492/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052492 Building REAL250005052493 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052493' /scratch/stefan/7921156/working/building/REAL250005052493 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052493 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052493/0 /scratch/stefan/7921156/working/building/REAL250005052493 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/633 `/scratch/stefan/7921156/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052493.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052493 none CSC=CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 163, 93, 93, 93, 65, 26, 63, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 163, 163, 93, 65, 65, 65, 65, 26, 26, 8, 1] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 638 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052493 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052493 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052493/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052493 Building REAL250005052494 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052494' /scratch/stefan/7921156/working/building/REAL250005052494 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052494 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052494/0 /scratch/stefan/7921156/working/building/REAL250005052494 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/634 `/scratch/stefan/7921156/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CO)CCC1) `REAL250005052494.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052494 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CO)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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 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, 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: [67, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 69, 115, 115, 115, 191, 201, 191, 191, 191, 69, 69, 69, 69, 21, 21, 8, 1, 115, 201, 201, 603, 191, 191, 191, 191, 191, 191] 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: 1328 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052494 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CO)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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 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, 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, 6, 27, 98, 185, 185, 185, 191, 191, 191, 191, 191, 6, 1, 6, 1, 1, 10, 1, 1, 1, 27, 27, 27, 27, 98, 98, 185, 191, 6, 10, 10, 30, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 37, 38, 13, 15, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 708 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052494 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052494 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052494/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052494 Building REAL250005052495 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052495' /scratch/stefan/7921156/working/building/REAL250005052495 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052495 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052495/0 /scratch/stefan/7921156/working/building/REAL250005052495 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/635 `/scratch/stefan/7921156/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)NC(=O)CCC(N)=O) `REAL250005052495.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052495 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 14, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 38, 54, 54, 54, 145, 187, 201, 201, 38, 38, 38, 38, 14, 14, 5, 1, 54, 145, 145, 187, 187, 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: 847 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052495 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052495 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052495/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052495 Building REAL250005052496 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052496' /scratch/stefan/7921156/working/building/REAL250005052496 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052496 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052496/0 /scratch/stefan/7921156/working/building/REAL250005052496 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/636 `/scratch/stefan/7921156/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005052496.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052496 none C=CCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 1, 1, 1, 7, 7, 7, 21, 21, 53, 141, 141, 141, 147, 147, 147, 147, 147, 1, 1, 18, 18, 18, 7, 7, 7, 21, 21, 21, 21, 53, 53, 141, 147, 1, 1, 1, 1] 201 rigid atoms, others: [35, 2, 3, 4, 37, 38, 19, 20, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 526 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052496 none C=CCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 147, 67, 67, 67, 39, 15, 39, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 147, 147, 201, 201, 201, 201, 201, 67, 39, 39, 39, 39, 15, 15, 4, 1, 147, 147, 147, 147] 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: 783 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052496 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052496 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052496/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052496 Building REAL250005052497 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052497' /scratch/stefan/7921156/working/building/REAL250005052497 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052497 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052497/0 /scratch/stefan/7921156/working/building/REAL250005052497 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/637 `/scratch/stefan/7921156/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)NC(=O)COC(F)F) `REAL250005052497.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052497 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COC(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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 40, 66, 66, 66, 137, 190, 201, 201, 40, 40, 40, 40, 13, 13, 4, 1, 66, 137, 137, 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]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052497 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052497 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052497/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052497 Building REAL250005052498 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052498' /scratch/stefan/7921156/working/building/REAL250005052498 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052498 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052498/0 /scratch/stefan/7921156/working/building/REAL250005052498 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/638 `/scratch/stefan/7921156/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCS1) `REAL250005052498.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052498 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.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, 1, 11, 1, 1, 5, 5, 14, 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, 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] 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, 38, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 75, 98, 98, 98, 104, 104, 104, 104, 75, 75, 75, 75, 38, 38, 10, 1, 98, 104, 104, 104, 104, 104] 104 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: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052498 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.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, 1, 11, 1, 1, 5, 5, 14, 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, 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] 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: [20, 8, 20, 59, 94, 94, 94, 104, 104, 104, 104, 104, 7, 1, 7, 1, 1, 1, 1, 1, 20, 20, 20, 20, 59, 59, 94, 104, 8, 1, 1, 1, 1, 1] 104 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 361 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052498 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052498 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052498/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052498 Building REAL250005052499 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052499' /scratch/stefan/7921156/working/building/REAL250005052499 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052499 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052499/0 /scratch/stefan/7921156/working/building/REAL250005052499 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/639 `/scratch/stefan/7921156/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052499.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052499 none CC1=NOC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 11, 37, 37, 91, 131, 131, 131, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 11, 37, 37, 37, 37, 91, 91, 131, 135, 1, 1] 135 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 35, 20, 21, 22, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 501 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052499 none CC1=NOC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 135, 102, 102, 102, 68, 28, 67, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 102, 68, 68, 68, 68, 28, 28, 10, 1, 135, 135] 135 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 482 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052499 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052499 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052499/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052499 Building REAL250005052500 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052500' /scratch/stefan/7921156/working/building/REAL250005052500 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052500 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052500/0 /scratch/stefan/7921156/working/building/REAL250005052500 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/640 `/scratch/stefan/7921156/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(=O)NC1CC1) `REAL250005052500.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052500 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 75, 129, 129, 129, 162, 162, 162, 201, 201, 75, 75, 75, 75, 24, 24, 7, 1, 129, 162, 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]) total number of confs: 738 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: REAL250005052500 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 22, 55, 146, 199, 199, 199, 201, 201, 201, 201, 201, 22, 6, 23, 6, 6, 1, 1, 1, 1, 55, 55, 55, 55, 146, 146, 199, 201, 23, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 775 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052500 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052500 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052500/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052500 Building REAL250005052501 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052501' /scratch/stefan/7921156/working/building/REAL250005052501 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052501 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052501/0 /scratch/stefan/7921156/working/building/REAL250005052501 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/641 `/scratch/stefan/7921156/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)NC(=O)C1=CC(N)=NN1) `REAL250005052501.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052501 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(N)=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [44, 18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 44, 69, 69, 69, 77, 77, 77, 77, 77, 44, 44, 44, 44, 18, 18, 9, 1, 69, 77, 77, 77, 77] 77 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: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052501 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(N)=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 17, 47, 72, 72, 72, 77, 77, 77, 77, 77, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 47, 47, 72, 77, 7, 1, 1, 1, 1] 77 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052501 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052501 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052501/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052501 Building REAL250005052502 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052502' /scratch/stefan/7921156/working/building/REAL250005052502 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052502 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052502/0 /scratch/stefan/7921156/working/building/REAL250005052502 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/642 `/scratch/stefan/7921156/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCSC1) `REAL250005052502.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052502 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCSC1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [67, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 107, 107, 107, 163, 163, 163, 163, 69, 69, 69, 69, 27, 27, 10, 1, 107, 163, 163, 163, 163, 163, 163, 163] 163 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: 580 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: REAL250005052502 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCSC1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [34, 10, 34, 107, 155, 155, 155, 163, 163, 163, 163, 163, 10, 1, 10, 1, 1, 1, 1, 1, 34, 34, 34, 34, 107, 107, 155, 163, 10, 1, 1, 1, 1, 1, 1, 1] 163 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 590 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052502 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052502 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052502/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052502 Building REAL250005052503 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052503' /scratch/stefan/7921156/working/building/REAL250005052503 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052503 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052503/0 /scratch/stefan/7921156/working/building/REAL250005052503 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/643 `/scratch/stefan/7921156/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCO1) `REAL250005052503.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052503 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [60, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 61, 80, 80, 80, 85, 85, 85, 61, 61, 61, 61, 26, 26, 8, 1, 80, 85, 85, 85, 85, 85] 85 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]) total number of confs: 321 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: REAL250005052503 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 21, 54, 83, 83, 83, 85, 85, 85, 85, 85, 8, 1, 8, 1, 1, 1, 1, 21, 21, 21, 21, 54, 54, 83, 85, 8, 1, 1, 1, 1, 1] 85 rigid atoms, others: [32, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 308 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052503 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052503 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052503/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052503 Building REAL250005052504 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052504' /scratch/stefan/7921156/working/building/REAL250005052504 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052504 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052504/0 /scratch/stefan/7921156/working/building/REAL250005052504 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/644 `/scratch/stefan/7921156/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052504.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052504 none CCCC(O)CC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 507 conformations in input total number of sets (complete confs): 507 using faster count positions algorithm for large data unique positions, atoms: [169, 166, 141, 99, 141, 53, 53, 53, 33, 15, 33, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 169, 166, 166, 141, 423, 99, 99, 53, 33, 33, 33, 33, 15, 15, 4, 1] 507 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052504 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052504 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052504/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052504 Building REAL250005052505 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052505' /scratch/stefan/7921156/working/building/REAL250005052505 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052505 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052505/0 /scratch/stefan/7921156/working/building/REAL250005052505 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/645 `/scratch/stefan/7921156/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)CC#N) `REAL250005052505.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052505 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 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: [53, 17, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 55, 95, 95, 95, 164, 164, 164, 201, 201, 55, 55, 55, 55, 17, 17, 7, 1, 95, 164, 164, 164, 164, 164, 164, 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: 875 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052505 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052505 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052505/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052505 Building REAL250005052506 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052506' /scratch/stefan/7921156/working/building/REAL250005052506 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052506 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052506/0 /scratch/stefan/7921156/working/building/REAL250005052506 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/646 `/scratch/stefan/7921156/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(Cl)CC1) `REAL250005052506.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052506 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(Cl)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.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 16, 5, 5, 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, 3, 7, 3, 4, 7, 6, 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: [70, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 103, 103, 103, 169, 169, 169, 71, 71, 71, 71, 26, 26, 9, 1, 103, 169, 169, 169, 169] 169 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: 594 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: REAL250005052506 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(Cl)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.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 16, 5, 5, 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, 3, 7, 3, 4, 7, 6, 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: [46, 11, 46, 119, 165, 165, 165, 169, 169, 169, 169, 169, 11, 1, 11, 1, 1, 1, 1, 46, 46, 46, 46, 119, 119, 165, 169, 11, 1, 1, 1, 1] 169 rigid atoms, others: [13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 631 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052506 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052506 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052506/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052506 Building REAL250005052507 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052507' /scratch/stefan/7921156/working/building/REAL250005052507 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052507 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052507/0 /scratch/stefan/7921156/working/building/REAL250005052507 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/647 `/scratch/stefan/7921156/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCO1) `REAL250005052507.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052507 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 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, 7, 3, 7, 3, 4, 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 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [58, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 58, 80, 80, 80, 87, 87, 87, 87, 58, 58, 58, 58, 28, 28, 9, 1, 80, 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]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052507 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 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, 7, 3, 7, 3, 4, 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 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [22, 8, 22, 47, 78, 78, 78, 87, 87, 87, 87, 87, 8, 1, 8, 1, 1, 1, 1, 1, 22, 22, 22, 22, 47, 47, 78, 87, 8, 1, 1, 1, 1, 1] 87 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 292 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052507 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052507 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052507/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052507 Building REAL250005052508 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052508' /scratch/stefan/7921156/working/building/REAL250005052508 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052508 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052508/0 /scratch/stefan/7921156/working/building/REAL250005052508 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/648 `/scratch/stefan/7921156/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)NC(=O)C1(CO)COC1) `REAL250005052508.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052508 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CO)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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [73, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 75, 126, 126, 126, 194, 201, 194, 194, 194, 75, 75, 75, 75, 26, 26, 9, 1, 126, 201, 201, 603, 194, 194, 194, 194] 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]) total number of confs: 1323 number of broken/clashed sets: 217 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052508 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CO)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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [27, 6, 27, 85, 175, 176, 175, 194, 194, 194, 194, 194, 6, 1, 6, 1, 1, 7, 1, 1, 1, 27, 27, 27, 27, 85, 85, 176, 194, 6, 7, 7, 21, 1, 1, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 13, 15, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 663 number of broken/clashed sets: 217 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052508 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052508 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052508/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052508 Building REAL250005052509 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052509' /scratch/stefan/7921156/working/building/REAL250005052509 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052509 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052509/0 /scratch/stefan/7921156/working/building/REAL250005052509 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/649 `/scratch/stefan/7921156/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052509.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052509 none CC(C)=CCCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 177, 159, 66, 66, 66, 50, 20, 50, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 177, 177, 159, 159, 66, 50, 50, 50, 50, 20, 20, 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: 848 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052509 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052509 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052509/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052509 Building REAL250005052510 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052510' /scratch/stefan/7921156/working/building/REAL250005052510 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052510 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052510/0 /scratch/stefan/7921156/working/building/REAL250005052510 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/650 `/scratch/stefan/7921156/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC1) `REAL250005052510.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052510 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 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, 7, 3, 7, 3, 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 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [78, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 79, 116, 116, 116, 176, 176, 176, 79, 79, 79, 79, 29, 29, 10, 1, 116, 176, 176, 176, 176, 176] 176 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]) total number of confs: 634 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052510 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 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, 7, 3, 7, 3, 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 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [41, 11, 41, 114, 165, 165, 165, 176, 176, 176, 176, 176, 11, 1, 11, 1, 1, 1, 1, 41, 41, 41, 41, 114, 114, 165, 176, 11, 1, 1, 1, 1, 1] 176 rigid atoms, others: [32, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 654 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052510 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052510 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052510/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052510 Building REAL250005052511 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052511' /scratch/stefan/7921156/working/building/REAL250005052511 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052511 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052511/0 /scratch/stefan/7921156/working/building/REAL250005052511 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/651 `/scratch/stefan/7921156/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)NC(=O)C1CCC(C)O1) `REAL250005052511.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052511 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(C)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 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, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [69, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 71, 106, 106, 106, 130, 130, 130, 130, 130, 71, 71, 71, 71, 28, 28, 10, 1, 106, 130, 130, 130, 130, 130, 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, 36, 37, 38]) total number of confs: 467 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052511 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(C)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 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, 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: [30, 10, 30, 79, 127, 127, 127, 130, 130, 130, 130, 130, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 79, 79, 127, 130, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2] 130 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052511 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052511 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052511/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052511 Building REAL250005052512 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052512' /scratch/stefan/7921156/working/building/REAL250005052512 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052512 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052512/0 /scratch/stefan/7921156/working/building/REAL250005052512 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/652 `/scratch/stefan/7921156/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NNC=C1N) `REAL250005052512.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052512 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NNC=C1N NO_LONG_NAME dock atom types: ['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.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [66, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 67, 96, 96, 96, 96, 96, 96, 96, 96, 67, 67, 67, 67, 25, 25, 9, 1, 96, 96, 96, 96, 96] 96 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: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052512 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NNC=C1N NO_LONG_NAME dock atom types: ['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.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [14, 3, 14, 49, 91, 91, 91, 96, 96, 96, 96, 96, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 49, 49, 91, 96, 3, 1, 1, 1, 1] 96 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052512 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052512/1 /scratch/stefan/7921156/working/building/REAL250005052512 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/653 `/scratch/stefan/7921156/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=C(N)C=NN1) `REAL250005052512.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052512/1/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: REAL250005052512 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=C(N)C=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.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [54, 23, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 54, 75, 75, 75, 113, 113, 113, 113, 113, 54, 54, 54, 54, 23, 23, 10, 1, 75, 113, 113, 113, 113] 113 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: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052512 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=C(N)C=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.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [31, 9, 31, 72, 105, 105, 105, 113, 113, 113, 113, 113, 9, 1, 9, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 72, 72, 105, 113, 9, 2, 2, 1, 1] 113 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 407 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052512 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052512 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052512/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052512/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052512 Building REAL250005052513 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052513' /scratch/stefan/7921156/working/building/REAL250005052513 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052513 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052513/0 /scratch/stefan/7921156/working/building/REAL250005052513 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/654 `/scratch/stefan/7921156/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CCO) `REAL250005052513.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052513 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [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] 1 hydrogens need rotated 588 conformations in input total number of sets (complete confs): 588 using faster count positions algorithm for large data unique positions, atoms: [79, 34, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 79, 121, 121, 121, 181, 181, 196, 79, 79, 79, 79, 34, 34, 11, 1, 121, 181, 181, 196, 196, 588] 588 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]) total number of confs: 1340 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052513 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052513 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052513/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052513 Building REAL250005052514 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052514' /scratch/stefan/7921156/working/building/REAL250005052514 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052514 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052514/0 /scratch/stefan/7921156/working/building/REAL250005052514 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/655 `/scratch/stefan/7921156/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005052514.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052514 none CC1=NNC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 53, 103, 103, 103, 113, 113, 113, 113, 113, 1, 2, 2, 2, 1, 4, 14, 14, 14, 14, 53, 53, 103, 113] 113 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 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: REAL250005052514 none CC1=NNC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 113, 113, 73, 33, 73, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 113, 73, 73, 73, 73, 33, 33, 10, 1] 113 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: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052514 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052514/1 /scratch/stefan/7921156/working/building/REAL250005052514 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/656 `/scratch/stefan/7921156/working/3D/656' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005052514.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052514/1/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: REAL250005052514 none CC1=NN=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 49, 93, 93, 93, 101, 101, 101, 101, 101, 1, 2, 2, 2, 6, 15, 15, 15, 15, 49, 49, 93, 101, 1] 101 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 20] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 344 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: REAL250005052514 none CC1=NN=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 100, 100, 100, 78, 32, 78, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 100, 78, 78, 78, 78, 32, 32, 10, 1, 101] 101 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 375 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052514 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052514 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052514/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052514/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052514 Building REAL250005052515 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052515' /scratch/stefan/7921156/working/building/REAL250005052515 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052515 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052515/0 /scratch/stefan/7921156/working/building/REAL250005052515 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/657 `/scratch/stefan/7921156/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COC(=O)N1) `REAL250005052515.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052515 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COC(=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.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 6, 4, 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: [52, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 53, 75, 75, 75, 101, 101, 101, 101, 101, 53, 53, 53, 53, 22, 22, 9, 1, 75, 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]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052515 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COC(=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.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 6, 4, 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: [25, 8, 25, 62, 95, 95, 95, 101, 101, 101, 101, 101, 7, 1, 7, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 62, 62, 95, 101, 8, 1, 1] 101 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052515 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052515/1 /scratch/stefan/7921156/working/building/REAL250005052515 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/658 `/scratch/stefan/7921156/working/3D/658' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COC(=O)[N-]1) `REAL250005052515.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052515/1/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: REAL250005052515 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'H', 'H', '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, 1, 11, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 5, 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: [23, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 19, 19, 7, 1, 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]) 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: REAL250005052515 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'H', 'H', '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, 1, 11, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 21, 29, 29, 29, 34, 34, 34, 34, 34, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 21, 21, 29, 34, 4, 1] 34 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052515 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052515 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052515/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052515/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052515 Building REAL250005052516 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052516' /scratch/stefan/7921156/working/building/REAL250005052516 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052516 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052516/0 /scratch/stefan/7921156/working/building/REAL250005052516 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/659 `/scratch/stefan/7921156/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052516.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052516 none CC=CC(O)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 168, 115, 168, 115, 115, 77, 23, 75, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 168, 504, 115, 77, 77, 77, 77, 23, 23, 5, 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: 1348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052516 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052516 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052516/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052516 Building REAL250005052517 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052517' /scratch/stefan/7921156/working/building/REAL250005052517 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052517 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052517/0 /scratch/stefan/7921156/working/building/REAL250005052517 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/660 `/scratch/stefan/7921156/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052517.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052517 none CCCC[C@H](C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 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, 193, 180, 129, 48, 129, 129, 48, 48, 40, 15, 40, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 192, 193, 184, 184, 129, 129, 129, 48, 40, 40, 40, 40, 15, 15, 4, 1] 201 rigid atoms, others: [42, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 931 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052517 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052517 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052517/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052517 Building REAL250005052518 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052518' /scratch/stefan/7921156/working/building/REAL250005052518 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052518 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052518/0 /scratch/stefan/7921156/working/building/REAL250005052518 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/661 `/scratch/stefan/7921156/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)NC(=O)[C@H](C)[NH+](C)C) `REAL250005052518.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052518 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 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, 7, 7, 3, 7, 3, 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] 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: [14, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 16, 16, 16, 17, 17, 17, 14, 14, 14, 14, 13, 13, 8, 1, 14, 16, 16, 16, 17, 17, 17, 17, 17, 17] 17 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]) total number of confs: 68 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052518 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052518/1 /scratch/stefan/7921156/working/building/REAL250005052518 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/662 `/scratch/stefan/7921156/working/3D/662' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)N(C)C) `REAL250005052518.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052518/1/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: REAL250005052518 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 10, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [70, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 72, 96, 96, 96, 121, 121, 121, 123, 123, 72, 72, 72, 72, 31, 31, 10, 1, 96, 121, 121, 121, 123, 123, 123, 123, 123, 123] 123 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: 503 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052518 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052518 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052518/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052518/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052518 Building REAL250005052519 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052519' /scratch/stefan/7921156/working/building/REAL250005052519 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052519 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052519/0 /scratch/stefan/7921156/working/building/REAL250005052519 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/663 `/scratch/stefan/7921156/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(F)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052519.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052519 none CCC=C(F)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 149, 149, 110, 149, 110, 110, 66, 24, 65, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 149, 110, 66, 66, 66, 66, 24, 24, 7, 1] 201 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 845 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052519 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052519 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052519/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052519 Building REAL250005052520 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052520' /scratch/stefan/7921156/working/building/REAL250005052520 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052520 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052520/0 /scratch/stefan/7921156/working/building/REAL250005052520 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/664 `/scratch/stefan/7921156/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052520.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052520 none CCC=CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 163, 109, 109, 109, 66, 20, 64, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 163, 163, 109, 66, 66, 66, 66, 20, 20, 4, 1] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 838 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052520 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052520 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052520/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052520 Building REAL250005052521 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052521' /scratch/stefan/7921156/working/building/REAL250005052521 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052521 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052521/0 /scratch/stefan/7921156/working/building/REAL250005052521 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/665 `/scratch/stefan/7921156/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CNC(=O)C1) `REAL250005052521.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052521 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CNC(=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.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [72, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 74, 110, 110, 110, 166, 166, 166, 166, 166, 74, 74, 74, 74, 28, 28, 10, 1, 110, 166, 166, 166, 166, 166, 166] 166 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: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052521 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CNC(=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.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [35, 9, 35, 101, 156, 156, 156, 166, 166, 166, 166, 166, 9, 1, 9, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 101, 101, 156, 166, 9, 1, 1, 1, 1, 1, 1] 166 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 590 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052521 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052521 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052521/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052521 Building REAL250005052522 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052522' /scratch/stefan/7921156/working/building/REAL250005052522 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052522 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052522/0 /scratch/stefan/7921156/working/building/REAL250005052522 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/666 `/scratch/stefan/7921156/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)NC(=O)C1=NON=C1N) `REAL250005052522.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052522 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NON=C1N NO_LONG_NAME dock atom types: ['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.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 4, 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: [73, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 73, 107, 107, 107, 114, 114, 114, 114, 114, 73, 73, 73, 73, 31, 31, 7, 1, 107, 114, 114] 114 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]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052522 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NON=C1N NO_LONG_NAME dock atom types: ['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.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 4, 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: [18, 6, 18, 59, 107, 107, 107, 114, 114, 114, 114, 114, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 59, 59, 107, 114, 6, 1, 1] 114 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052522 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052522 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052522/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052522 Building REAL250005052523 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052523' /scratch/stefan/7921156/working/building/REAL250005052523 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052523 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052523/0 /scratch/stefan/7921156/working/building/REAL250005052523 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/667 `/scratch/stefan/7921156/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CNC(=O)N1) `REAL250005052523.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052523 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CNC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [67, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 67, 103, 103, 103, 123, 123, 123, 123, 123, 123, 67, 67, 67, 67, 30, 30, 9, 1, 103, 123, 123, 123, 123] 123 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]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052523 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CNC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [29, 10, 29, 78, 117, 117, 117, 123, 123, 123, 123, 123, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 78, 78, 117, 123, 10, 1, 1, 1, 1] 123 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 448 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052523 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052523 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052523/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052523 Building REAL250005052524 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052524' /scratch/stefan/7921156/working/building/REAL250005052524 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052524 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052524/0 /scratch/stefan/7921156/working/building/REAL250005052524 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/668 `/scratch/stefan/7921156/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)NC(=O)C1=CN=CS1) `REAL250005052524.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052524 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', '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, 1, 11, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [56, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 56, 81, 81, 81, 95, 95, 95, 95, 56, 56, 56, 56, 23, 23, 9, 1, 81, 95, 95] 95 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]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052524 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', '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, 1, 11, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [23, 8, 23, 52, 91, 91, 91, 95, 95, 95, 95, 95, 8, 1, 8, 1, 1, 1, 1, 1, 23, 23, 23, 23, 52, 52, 91, 95, 9, 1, 1] 95 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 345 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052524 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052524 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052524/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052524 Building REAL250005052525 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052525' /scratch/stefan/7921156/working/building/REAL250005052525 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052525 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052525/0 /scratch/stefan/7921156/working/building/REAL250005052525 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/669 `/scratch/stefan/7921156/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)NC(=O)CCN=[N+]=[N-]) `REAL250005052525.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052525 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 8, 8, 8, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 10, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 28, 45, 45, 45, 135, 170, 201, 201, 28, 28, 28, 28, 10, 10, 4, 1, 45, 135, 135, 170, 170] 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]) total number of confs: 775 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052525 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052525 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052525/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052525 Building REAL250005052526 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052526' /scratch/stefan/7921156/working/building/REAL250005052526 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052526 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052526/0 /scratch/stefan/7921156/working/building/REAL250005052526 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/670 `/scratch/stefan/7921156/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052526.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052526 none C#CCOCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 151, 105, 57, 57, 57, 32, 9, 32, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 105, 105, 57, 32, 32, 32, 32, 9, 9, 3, 1] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 815 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052526 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052526 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052526/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052526 Building REAL250005052527 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052527' /scratch/stefan/7921156/working/building/REAL250005052527 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052527 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052527/0 /scratch/stefan/7921156/working/building/REAL250005052527 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/671 `/scratch/stefan/7921156/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)NC(=O)CC1=NN=CO1) `REAL250005052527.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052527 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=NN=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.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 38, 58, 58, 58, 147, 201, 201, 201, 201, 38, 38, 38, 38, 15, 15, 5, 1, 58, 147, 147, 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]) 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: REAL250005052527 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=NN=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.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 32, 74, 151, 200, 200, 200, 201, 201, 201, 201, 201, 32, 4, 32, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 151, 151, 200, 201, 32, 4, 4, 1] 201 rigid atoms, others: [32, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 813 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052527 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052527 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052527/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052527 Building REAL250005052528 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052528' /scratch/stefan/7921156/working/building/REAL250005052528 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052528 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052528/0 /scratch/stefan/7921156/working/building/REAL250005052528 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/672 `/scratch/stefan/7921156/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)NC(=O)C1CCCS1) `REAL250005052528.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052528 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 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, 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 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [62, 22, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 63, 91, 91, 91, 127, 127, 127, 127, 63, 63, 63, 63, 22, 22, 8, 1, 91, 127, 127, 127, 127, 127, 127, 127] 127 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: 453 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052528 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 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, 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 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [35, 10, 35, 91, 124, 124, 124, 127, 127, 127, 127, 127, 10, 1, 10, 1, 1, 1, 1, 1, 35, 35, 35, 35, 91, 91, 124, 127, 10, 1, 1, 1, 1, 1, 1, 1] 127 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052528 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052528 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052528/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052528 Building REAL250005052529 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052529' /scratch/stefan/7921156/working/building/REAL250005052529 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052529 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052529/0 /scratch/stefan/7921156/working/building/REAL250005052529 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/673 `/scratch/stefan/7921156/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052529.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052529 none COC(C)(C)CC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 184, 129, 184, 184, 71, 71, 71, 46, 17, 46, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 199, 199, 199, 184, 184, 184, 184, 184, 184, 129, 129, 71, 46, 46, 46, 46, 17, 17, 5, 1] 199 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 866 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052529 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052529 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052529/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052529 Building REAL250005052530 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052530' /scratch/stefan/7921156/working/building/REAL250005052530 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052530 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052530/0 /scratch/stefan/7921156/working/building/REAL250005052530 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/674 `/scratch/stefan/7921156/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052530.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052530 none CC(O)CCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 426 conformations in input total number of sets (complete confs): 426 using faster count positions algorithm for large data unique positions, atoms: [142, 118, 142, 117, 67, 67, 67, 48, 23, 48, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 142, 142, 142, 139, 426, 125, 125, 117, 117, 67, 48, 48, 48, 48, 23, 23, 8, 1] 426 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: 1079 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052530 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052530 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052530/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052530 Building REAL250005052531 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052531' /scratch/stefan/7921156/working/building/REAL250005052531 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052531 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052531/0 /scratch/stefan/7921156/working/building/REAL250005052531 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/675 `/scratch/stefan/7921156/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=CC=C1) `REAL250005052531.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052531 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=CC=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 23, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 66, 100, 100, 100, 200, 201, 201, 201, 201, 66, 66, 66, 66, 23, 23, 8, 1, 100, 200, 200, 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: 814 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052531 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=CC=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 25, 72, 152, 192, 192, 192, 201, 201, 201, 201, 201, 25, 5, 25, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 152, 152, 192, 201, 25, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 789 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052531 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052531 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052531/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052531 Building REAL250005052532 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052532' /scratch/stefan/7921156/working/building/REAL250005052532 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052532 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052532/0 /scratch/stefan/7921156/working/building/REAL250005052532 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/676 `/scratch/stefan/7921156/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052532.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052532 none C#CCCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 106, 106, 106, 66, 22, 65, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 191, 191, 106, 66, 66, 66, 66, 22, 22, 5, 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: 832 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052532 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052532 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052532/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052532 Building REAL250005052533 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052533' /scratch/stefan/7921156/working/building/REAL250005052533 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052533 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052533/0 /scratch/stefan/7921156/working/building/REAL250005052533 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/677 `/scratch/stefan/7921156/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005052533.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052533 none CC(=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 100, 100, 100, 65, 21, 63, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 192, 201, 201, 192, 192, 192, 192, 100, 65, 65, 65, 65, 21, 21, 6, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 713 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052533 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052533 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052533/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052533 Building REAL250005052534 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052534' /scratch/stefan/7921156/working/building/REAL250005052534 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052534 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052534/0 /scratch/stefan/7921156/working/building/REAL250005052534 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/678 `/scratch/stefan/7921156/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(CC(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005052534.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052534 none COC1(CC(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 10, 45, 45, 45, 94, 94, 126, 194, 194, 194, 196, 196, 196, 196, 196, 1, 1, 6, 6, 6, 10, 10, 45, 94, 94, 94, 94, 126, 126, 194, 196, 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: 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: REAL250005052534 none COC1(CC(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 141, 53, 53, 53, 47, 16, 47, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 196, 196, 201, 201, 201, 141, 141, 53, 47, 47, 47, 47, 16, 16, 4, 1, 196, 196, 196, 196] 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: 803 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052534 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052534 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052534/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052534 Building REAL250005052535 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052535' /scratch/stefan/7921156/working/building/REAL250005052535 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052535 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052535/0 /scratch/stefan/7921156/working/building/REAL250005052535 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/679 `/scratch/stefan/7921156/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052535.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052535 none CC[C@H](C)[C@H](O)C(=O)NC(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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 193, 166, 193, 192, 113, 166, 166, 113, 113, 71, 25, 69, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 193, 498, 113, 71, 71, 71, 71, 25, 25, 6, 1] 603 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1365 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052535 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052535 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052535/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052535 Building REAL250005052536 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052536' /scratch/stefan/7921156/working/building/REAL250005052536 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052536 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052536/0 /scratch/stefan/7921156/working/building/REAL250005052536 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/680 `/scratch/stefan/7921156/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052536.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052536 none CC=CC=CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [185, 185, 177, 177, 113, 113, 113, 75, 27, 72, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 185, 185, 185, 185, 185, 177, 177, 113, 75, 75, 75, 75, 27, 27, 9, 1] 185 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: 690 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052536 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052536 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052536/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052536 Building REAL250005052537 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052537' /scratch/stefan/7921156/working/building/REAL250005052537 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052537 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052537/0 /scratch/stefan/7921156/working/building/REAL250005052537 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/681 `/scratch/stefan/7921156/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)NC(=O)C1=NC=NN1C) `REAL250005052537.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052537 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=NN1C NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 1, 8, 8, 5, 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, 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] 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: [85, 37, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 86, 123, 123, 123, 124, 124, 124, 124, 124, 86, 86, 86, 86, 37, 37, 9, 1, 123, 124, 124, 124, 124] 124 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: 467 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052537 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=NN1C NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 16, 60, 116, 116, 116, 124, 124, 124, 124, 124, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 60, 60, 116, 124, 5, 1, 2, 2, 2] 124 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 430 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052537 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052537 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052537/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052537 Building REAL250005052538 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052538' /scratch/stefan/7921156/working/building/REAL250005052538 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052538 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052538/0 /scratch/stefan/7921156/working/building/REAL250005052538 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/682 `/scratch/stefan/7921156/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)NC(=O)[C@@H]1CC[C@@H](O)C1) `REAL250005052538.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052538 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC[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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [75, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 76, 128, 128, 128, 201, 201, 201, 201, 201, 201, 201, 76, 76, 76, 76, 28, 28, 8, 1, 128, 201, 201, 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: 1306 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: REAL250005052538 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC[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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [42, 10, 42, 132, 193, 193, 193, 201, 201, 201, 201, 201, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 132, 132, 193, 201, 10, 1, 1, 1, 1, 6, 1, 1] 603 rigid atoms, others: [32, 33, 34, 35, 37, 38, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 741 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052538 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052538 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052538/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052538 Building REAL250005052539 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052539' /scratch/stefan/7921156/working/building/REAL250005052539 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052539 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052539/0 /scratch/stefan/7921156/working/building/REAL250005052539 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/683 `/scratch/stefan/7921156/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC=CCC1) `REAL250005052539.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052539 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [87, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 88, 139, 139, 139, 201, 201, 201, 201, 201, 201, 88, 88, 88, 88, 31, 31, 9, 1, 139, 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]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052539 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [42, 11, 42, 123, 191, 191, 191, 201, 201, 201, 201, 201, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 123, 123, 191, 201, 11, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 714 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052539 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052539 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052539/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052539 Building REAL250005052540 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052540' /scratch/stefan/7921156/working/building/REAL250005052540 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052540 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052540/0 /scratch/stefan/7921156/working/building/REAL250005052540 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/684 `/scratch/stefan/7921156/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052540.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052540 none COCC=CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 105, 105, 48, 48, 48, 30, 10, 30, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 191, 191, 105, 105, 48, 30, 30, 30, 30, 10, 10, 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: 768 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052540 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052540 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052540/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052540 Building REAL250005052541 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052541' /scratch/stefan/7921156/working/building/REAL250005052541 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052541 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052541/0 /scratch/stefan/7921156/working/building/REAL250005052541 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/685 `/scratch/stefan/7921156/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC2CC2C1) `REAL250005052541.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052541 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC2CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 69, 110, 110, 110, 201, 201, 201, 201, 201, 69, 69, 69, 69, 28, 28, 8, 1, 110, 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]) total number of confs: 673 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: REAL250005052541 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC2CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 11, 41, 120, 194, 194, 194, 201, 201, 201, 201, 201, 11, 1, 11, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 120, 120, 194, 201, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 713 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052541 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052541 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052541/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052541 Building REAL250005052542 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052542' /scratch/stefan/7921156/working/building/REAL250005052542 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052542 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052542/0 /scratch/stefan/7921156/working/building/REAL250005052542 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/686 `/scratch/stefan/7921156/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1CC(C)C1) `REAL250005052542.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052542 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1CC(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.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 71, 122, 122, 122, 189, 201, 201, 201, 201, 71, 71, 71, 71, 21, 21, 4, 1, 122, 189, 189, 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]) total number of confs: 816 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: REAL250005052542 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1CC(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.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 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, 142, 201, 201, 201, 201, 201, 201, 201, 201, 26, 6, 26, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 142, 142, 201, 201, 26, 6, 6, 1, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 33, 34, 38, 39, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 786 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052542 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052542/1 /scratch/stefan/7921156/working/building/REAL250005052542 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/687 `/scratch/stefan/7921156/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[NH+]1CC(C)C1) `REAL250005052542.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052542/1/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: REAL250005052542 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[NH+]1CC(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.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 12, 12, 12, 12, 12, 12, 9, 9, 9, 9, 8, 8, 7, 1, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 12 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: 43 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: REAL250005052542 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[NH+]1CC(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.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 8, 10, 10, 10, 10, 12, 12, 12, 12, 12, 7, 4, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 10, 10, 10, 12, 7, 4, 4, 1, 1, 1, 2, 2, 2, 1, 1] 12 rigid atoms, others: [33, 34, 35, 39, 40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 51 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052542 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052542 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052542/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052542/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052542 Building REAL250005052543 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052543' /scratch/stefan/7921156/working/building/REAL250005052543 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052543 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052543/0 /scratch/stefan/7921156/working/building/REAL250005052543 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/688 `/scratch/stefan/7921156/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052543.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052543 none CCC(C)(O)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 570 conformations in input total number of sets (complete confs): 570 using faster count positions algorithm for large data unique positions, atoms: [181, 164, 101, 164, 164, 101, 101, 61, 23, 59, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 190, 190, 190, 190, 190, 164, 164, 164, 492, 101, 61, 61, 61, 61, 23, 23, 8, 1] 570 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: 1377 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052543 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052543 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052543/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052543 Building REAL250005052544 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052544' /scratch/stefan/7921156/working/building/REAL250005052544 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052544 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052544/0 /scratch/stefan/7921156/working/building/REAL250005052544 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/689 `/scratch/stefan/7921156/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052544.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052544 none C#CCC(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 97, 166, 97, 97, 62, 20, 59, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 166, 166, 166, 166, 97, 62, 62, 62, 62, 20, 20, 4, 1] 201 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 922 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052544 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052544 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052544/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052544 Building REAL250005052545 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052545' /scratch/stefan/7921156/working/building/REAL250005052545 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052545 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052545/0 /scratch/stefan/7921156/working/building/REAL250005052545 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/690 `/scratch/stefan/7921156/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052545.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052545 none C=CC(O)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 131, 200, 131, 131, 77, 27, 75, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 600, 131, 77, 77, 77, 77, 27, 27, 8, 1] 603 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 1426 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052545 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052545 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052545/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052545 Building REAL250005052546 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052546' /scratch/stefan/7921156/working/building/REAL250005052546 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052546 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052546/0 /scratch/stefan/7921156/working/building/REAL250005052546 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/691 `/scratch/stefan/7921156/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)NC(=O)CCCN=[N+]=[N-]) `REAL250005052546.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052546 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCN=[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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 8, 8, 8, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 19, 25, 25, 25, 75, 76, 146, 201, 201, 19, 19, 19, 19, 11, 11, 4, 1, 25, 75, 75, 98, 98, 138, 130] 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: 832 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052546 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052546 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052546/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052546 Building REAL250005052547 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052547' /scratch/stefan/7921156/working/building/REAL250005052547 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052547 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052547/0 /scratch/stefan/7921156/working/building/REAL250005052547 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/692 `/scratch/stefan/7921156/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)NC(=O)C1OCC1(C)C) `REAL250005052547.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052547 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1OCC1(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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [74, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 75, 97, 97, 97, 100, 100, 100, 100, 100, 75, 75, 75, 75, 34, 34, 9, 1, 97, 100, 100, 100, 100, 100, 100, 100, 100, 100] 100 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: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052547 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1OCC1(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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 15, 50, 90, 90, 90, 100, 100, 100, 100, 100, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 90, 100, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2] 100 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052547 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052547 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052547/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052547 Building REAL250005052548 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052548' /scratch/stefan/7921156/working/building/REAL250005052548 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052548 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052548/0 /scratch/stefan/7921156/working/building/REAL250005052548 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/693 `/scratch/stefan/7921156/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)NC(=O)C12CC1CC2) `REAL250005052548.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052548 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [74, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 75, 95, 95, 95, 200, 200, 200, 200, 75, 75, 75, 75, 32, 32, 11, 1, 95, 200, 200, 200, 200, 200, 200, 200] 200 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: 512 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052548 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [35, 7, 35, 113, 188, 188, 188, 200, 200, 200, 200, 200, 7, 1, 7, 1, 1, 1, 1, 1, 35, 35, 35, 35, 113, 113, 188, 200, 7, 1, 1, 1, 1, 1, 1, 1] 200 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 697 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052548 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052548 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052548/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052548 Building REAL250005052549 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052549' /scratch/stefan/7921156/working/building/REAL250005052549 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052549 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052549/0 /scratch/stefan/7921156/working/building/REAL250005052549 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/694 `/scratch/stefan/7921156/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052549.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052549 none CCCC(C)=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 127, 127, 127, 64, 64, 64, 38, 14, 38, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 127, 127, 127, 127, 64, 38, 38, 38, 38, 14, 14, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 829 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052549 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052549 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052549/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052549 Building REAL250005052550 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052550' /scratch/stefan/7921156/working/building/REAL250005052550 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052550 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052550/0 /scratch/stefan/7921156/working/building/REAL250005052550 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/695 `/scratch/stefan/7921156/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@H](C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052550.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052550 none C=C[C@H](C)CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 147, 201, 199, 66, 66, 66, 49, 18, 49, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 147, 147, 66, 49, 49, 49, 49, 18, 18, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 903 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052550 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052550 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052550/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052550 Building REAL250005052551 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052551' /scratch/stefan/7921156/working/building/REAL250005052551 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052551 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052551/0 /scratch/stefan/7921156/working/building/REAL250005052551 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/696 `/scratch/stefan/7921156/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)NC(=O)C=CC1CC1) `REAL250005052551.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052551 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [60, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 60, 90, 90, 90, 164, 164, 201, 201, 60, 60, 60, 60, 21, 21, 5, 1, 90, 164, 164, 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: 716 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052551 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [99, 46, 99, 161, 201, 201, 201, 201, 201, 201, 201, 201, 46, 10, 45, 10, 1, 1, 1, 1, 99, 99, 99, 99, 161, 161, 201, 201, 46, 10, 10, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 786 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052551 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052551 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052551/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052551 Building REAL250005052552 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052552' /scratch/stefan/7921156/working/building/REAL250005052552 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052552 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052552/0 /scratch/stefan/7921156/working/building/REAL250005052552 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/697 `/scratch/stefan/7921156/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C=NO1) `REAL250005052552.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052552 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 12, 34, 34, 84, 119, 119, 119, 126, 126, 126, 126, 126, 1, 1, 1, 2, 2, 2, 12, 34, 34, 34, 34, 84, 84, 119, 126, 1] 126 rigid atoms, others: [0, 1, 2, 3, 33, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 471 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: REAL250005052552 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 83, 83, 83, 54, 24, 54, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 126, 83, 54, 54, 54, 54, 24, 24, 9, 1, 126] 126 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 376 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052552 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052552 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052552/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052552 Building REAL250005052553 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052553' /scratch/stefan/7921156/working/building/REAL250005052553 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052553 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052553/0 /scratch/stefan/7921156/working/building/REAL250005052553 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/698 `/scratch/stefan/7921156/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052553.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052553 none CC(C)CC(=O)C(=O)NC(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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 136, 97, 136, 97, 97, 49, 15, 47, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 195, 195, 97, 49, 49, 49, 49, 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: 849 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052553 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052553 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052553/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052553 Building REAL250005052554 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052554' /scratch/stefan/7921156/working/building/REAL250005052554 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052554 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052554/0 /scratch/stefan/7921156/working/building/REAL250005052554 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/699 `/scratch/stefan/7921156/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C#N)CC1C) `REAL250005052554.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052554 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C#N)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [44, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 44, 62, 62, 62, 75, 75, 75, 75, 75, 44, 44, 44, 44, 18, 18, 8, 1, 62, 75, 75, 75, 75, 75, 75] 75 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: 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: REAL250005052554 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C#N)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [15, 4, 15, 42, 72, 72, 72, 75, 75, 75, 75, 75, 4, 1, 4, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 42, 42, 72, 75, 4, 1, 1, 1, 2, 2, 2] 75 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052554 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052554 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052554/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052554 Building REAL250005052555 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052555' /scratch/stefan/7921156/working/building/REAL250005052555 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052555 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052555/0 /scratch/stefan/7921156/working/building/REAL250005052555 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/700 `/scratch/stefan/7921156/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C#N)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052555.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052555 none CCC(C#N)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [172, 161, 89, 161, 161, 89, 89, 56, 26, 56, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 181, 161, 89, 56, 56, 56, 56, 26, 26, 10, 1] 181 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: 814 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052555 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052555 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052555/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052555 Building REAL250005052556 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052556' /scratch/stefan/7921156/working/building/REAL250005052556 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052556 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052556/0 /scratch/stefan/7921156/working/building/REAL250005052556 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/701 `/scratch/stefan/7921156/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)NC(=O)[C@@H]1CNC(=O)O1) `REAL250005052556.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052556 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CNC(=O)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [73, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 75, 126, 126, 126, 148, 148, 148, 148, 148, 148, 75, 75, 75, 75, 31, 31, 11, 1, 126, 148, 148, 148] 148 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]) 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: REAL250005052556 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CNC(=O)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [35, 10, 35, 96, 137, 137, 137, 148, 148, 148, 148, 148, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 96, 96, 137, 148, 10, 1, 1, 1] 148 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 539 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052556 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052556 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052556/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052556 Building REAL250005052557 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052557' /scratch/stefan/7921156/working/building/REAL250005052557 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052557 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052557/0 /scratch/stefan/7921156/working/building/REAL250005052557 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/702 `/scratch/stefan/7921156/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1C2CCC21) `REAL250005052557.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052557 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [63, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 65, 100, 100, 100, 126, 126, 126, 126, 65, 65, 65, 65, 29, 29, 9, 1, 100, 126, 126, 126, 126, 126, 126, 126] 126 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: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052557 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 27, 74, 118, 118, 118, 126, 126, 126, 126, 126, 9, 1, 9, 1, 1, 1, 1, 1, 27, 27, 27, 27, 74, 74, 118, 126, 9, 1, 1, 1, 1, 1, 1, 1] 126 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 443 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052557 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052557 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052557/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052557 Building REAL250005052558 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052558' /scratch/stefan/7921156/working/building/REAL250005052558 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052558 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052558/0 /scratch/stefan/7921156/working/building/REAL250005052558 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/703 `/scratch/stefan/7921156/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052558.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052558 none C=C1CCC1C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 123, 189, 189, 189, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 10, 40, 40, 40, 40, 123, 123, 189, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 717 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: REAL250005052558 none C=C1CCC1C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 87, 35, 85, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 128, 87, 87, 87, 87, 35, 35, 10, 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: 708 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052558 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052558 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052558/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052558 Building REAL250005052559 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052559' /scratch/stefan/7921156/working/building/REAL250005052559 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052559 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052559/0 /scratch/stefan/7921156/working/building/REAL250005052559 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/704 `/scratch/stefan/7921156/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1[C@H](C)[C@@H]1C) `REAL250005052559.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052559 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [73, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 75, 112, 112, 112, 201, 201, 201, 201, 201, 201, 75, 75, 75, 75, 25, 25, 8, 1, 112, 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]) total number of confs: 696 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: REAL250005052559 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [47, 13, 47, 128, 196, 197, 196, 201, 201, 201, 201, 201, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 128, 128, 197, 201, 13, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 750 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052559 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052559 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052559/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052559 Building REAL250005052560 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052560' /scratch/stefan/7921156/working/building/REAL250005052560 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005052560 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052560/0 /scratch/stefan/7921156/working/building/REAL250005052560 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/705 `/scratch/stefan/7921156/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052560.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052560 none CC[N@H+](C)CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 32, 35, 35, 27, 27, 27, 20, 12, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 32, 32, 27, 20, 20, 20, 20, 12, 12, 4, 1] 35 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: 157 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052560 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052560/1 /scratch/stefan/7921156/working/building/REAL250005052560 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/706 `/scratch/stefan/7921156/working/3D/706' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052560.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052560/1/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: REAL250005052560 none CC[N@@H+](C)CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 30, 31, 31, 27, 27, 27, 20, 11, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 30, 30, 27, 20, 20, 20, 20, 11, 11, 4, 1] 31 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: 133 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052560 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `2' /scratch/stefan/7921156/working/building/REAL250005052560/2 /scratch/stefan/7921156/working/building/REAL250005052560 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 2 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/707 `/scratch/stefan/7921156/working/3D/707' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052560.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005052560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052560/2/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: REAL250005052560 none CCN(C)CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 147, 142, 147, 114, 114, 114, 72, 25, 68, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 157, 147, 147, 147, 142, 142, 114, 72, 72, 72, 72, 25, 25, 7, 1] 157 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: 673 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052560 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052560 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052560/0.* 2: /scratch/stefan/7921156/working/building/REAL250005052560/2.* 1: /scratch/stefan/7921156/working/building/REAL250005052560/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052560 Building REAL250005052561 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052561' /scratch/stefan/7921156/working/building/REAL250005052561 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052561 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052561/0 /scratch/stefan/7921156/working/building/REAL250005052561 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/708 `/scratch/stefan/7921156/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC2(C1)N=N2) `REAL250005052561.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052561 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC2(C1)N=N2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 1, 11, 5, 5, 5, 5, 8, 8, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [82, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 84, 122, 122, 122, 192, 192, 192, 192, 192, 84, 84, 84, 84, 34, 34, 11, 1, 122, 192, 192, 192, 192, 192] 192 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: 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: REAL250005052561 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC2(C1)N=N2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 1, 11, 5, 5, 5, 5, 8, 8, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [37, 11, 37, 127, 182, 182, 182, 192, 192, 192, 192, 192, 11, 1, 11, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 127, 127, 182, 192, 11, 1, 1, 1, 1, 1] 192 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 700 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052561 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052561 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052561/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052561 Building REAL250005052562 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052562' /scratch/stefan/7921156/working/building/REAL250005052562 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052562 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052562/0 /scratch/stefan/7921156/working/building/REAL250005052562 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/709 `/scratch/stefan/7921156/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052562.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052562 none CC(O)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 372 conformations in input total number of sets (complete confs): 372 using faster count positions algorithm for large data unique positions, atoms: [124, 117, 124, 117, 117, 84, 38, 83, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 372, 117, 84, 84, 84, 84, 38, 38, 11, 1] 372 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: 851 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052562 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052562 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052562/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052562 Building REAL250005052563 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052563' /scratch/stefan/7921156/working/building/REAL250005052563 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052563 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052563/0 /scratch/stefan/7921156/working/building/REAL250005052563 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/710 `/scratch/stefan/7921156/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052563.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052563 none CC(=O)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 93, 103, 93, 93, 70, 30, 68, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 103, 103, 103, 93, 70, 70, 70, 70, 30, 30, 9, 1] 103 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052563 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052563 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052563/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052563 Building REAL250005052564 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052564' /scratch/stefan/7921156/working/building/REAL250005052564 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052564 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052564/0 /scratch/stefan/7921156/working/building/REAL250005052564 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/711 `/scratch/stefan/7921156/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNN=C1N) `REAL250005052564.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052564 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNN=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [49, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 50, 68, 68, 68, 77, 77, 77, 77, 77, 50, 50, 50, 50, 21, 21, 9, 1, 68, 77, 77, 77, 77] 77 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: 272 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: REAL250005052564 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNN=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 52, 72, 72, 72, 77, 77, 77, 77, 77, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 52, 52, 72, 77, 8, 1, 1, 1, 1] 77 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 286 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052564 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052564 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052564/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052564 Building REAL250005052565 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052565' /scratch/stefan/7921156/working/building/REAL250005052565 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052565 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052565/0 /scratch/stefan/7921156/working/building/REAL250005052565 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/712 `/scratch/stefan/7921156/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)NC(N)=O) `REAL250005052565.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052565 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)NC(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.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [80, 36, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 80, 120, 120, 120, 178, 178, 188, 188, 188, 80, 80, 80, 80, 36, 36, 11, 1, 120, 178, 178, 178, 178, 188, 188, 188] 188 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: 780 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052565 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052565 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052565/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052565 Building REAL250005052566 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052566' /scratch/stefan/7921156/working/building/REAL250005052566 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052566 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052566/0 /scratch/stefan/7921156/working/building/REAL250005052566 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/713 `/scratch/stefan/7921156/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052566.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052566 none CCOC(=O)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 130, 130, 52, 130, 34, 34, 34, 22, 13, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 52, 52, 34, 22, 22, 22, 22, 13, 13, 4, 1] 133 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: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052566 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052566 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052566/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052566 Building REAL250005052567 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052567' /scratch/stefan/7921156/working/building/REAL250005052567 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052567 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052567/0 /scratch/stefan/7921156/working/building/REAL250005052567 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/714 `/scratch/stefan/7921156/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(=O)N[N-]1) `REAL250005052567.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052567 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(=O)N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'H', 'H', 'H', '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, 1, 11, 1, 1, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 6, 4, 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: [26, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 26, 33, 33, 33, 33, 33, 33, 33, 33, 26, 26, 26, 26, 21, 21, 7, 1, 33, 33, 33] 33 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052567 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(=O)N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'H', 'H', 'H', '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, 1, 11, 1, 1, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 6, 4, 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: [8, 3, 8, 18, 27, 27, 27, 33, 33, 33, 33, 33, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 18, 18, 27, 33, 3, 1, 1] 33 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052567 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052567 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052567/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052567 Building REAL250005052568 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052568' /scratch/stefan/7921156/working/building/REAL250005052568 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052568 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052568/0 /scratch/stefan/7921156/working/building/REAL250005052568 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/715 `/scratch/stefan/7921156/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=CN1) `REAL250005052568.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052568 none CC1=CC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 23, 23, 98, 168, 168, 168, 179, 179, 179, 179, 179, 1, 1, 2, 2, 2, 1, 5, 23, 23, 23, 23, 98, 98, 168, 179, 1, 1] 179 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 615 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: REAL250005052568 none CC1=CC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 124, 124, 124, 86, 34, 85, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 179, 179, 179, 179, 179, 179, 124, 86, 86, 86, 86, 34, 34, 10, 1, 179, 179] 179 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: 575 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052568 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052568 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052568/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052568 Building REAL250005052569 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052569' /scratch/stefan/7921156/working/building/REAL250005052569 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052569 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052569/0 /scratch/stefan/7921156/working/building/REAL250005052569 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/716 `/scratch/stefan/7921156/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005052569.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052569 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 9, 9, 9, 38, 38, 117, 177, 177, 177, 188, 188, 188, 188, 188, 1, 1, 1, 2, 2, 2, 9, 38, 38, 38, 38, 117, 117, 177, 188, 1, 1, 1, 1, 1, 1] 188 rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 33, 34, 18, 19, 20, 38] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 684 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: REAL250005052569 none CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 114, 114, 114, 75, 31, 73, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 188, 188, 114, 75, 75, 75, 75, 31, 31, 9, 1, 188, 188, 188, 188, 188, 188] 188 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 556 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052569 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052569 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052569/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052569 Building REAL250005052570 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052570' /scratch/stefan/7921156/working/building/REAL250005052570 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052570 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052570/0 /scratch/stefan/7921156/working/building/REAL250005052570 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/717 `/scratch/stefan/7921156/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCC#N) `REAL250005052570.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052570 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCC#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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 8, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 15, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 34, 55, 55, 55, 147, 163, 201, 201, 34, 34, 34, 34, 15, 15, 5, 1, 55, 147, 147, 180, 180, 199, 193] 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: 978 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052570 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052570 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052570/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052570 Building REAL250005052571 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052571' /scratch/stefan/7921156/working/building/REAL250005052571 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052571 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052571/0 /scratch/stefan/7921156/working/building/REAL250005052571 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/718 `/scratch/stefan/7921156/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C#N)CC1) `REAL250005052571.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052571 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 5, 5, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [44, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 44, 63, 63, 63, 95, 95, 95, 95, 44, 44, 44, 44, 18, 18, 8, 1, 63, 95, 95, 95, 95] 95 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]) total number of confs: 334 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: REAL250005052571 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 5, 5, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 20, 60, 92, 92, 92, 95, 95, 95, 95, 95, 6, 1, 6, 1, 1, 1, 1, 1, 20, 20, 20, 20, 60, 60, 92, 95, 6, 1, 1, 1, 1] 95 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 349 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052571 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052571 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052571/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052571 Building REAL250005052572 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052572' /scratch/stefan/7921156/working/building/REAL250005052572 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052572 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052572/0 /scratch/stefan/7921156/working/building/REAL250005052572 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/719 `/scratch/stefan/7921156/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052572.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052572 none C=C1CC(C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 11, 48, 48, 127, 189, 189, 189, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 11, 48, 48, 48, 48, 127, 127, 189, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 19, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 719 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052572 none C=C1CC(C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 123, 123, 79, 33, 78, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 123, 79, 79, 79, 79, 33, 33, 11, 1, 201, 201] 201 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 707 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052572 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052572 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052572/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052572 Building REAL250005052573 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052573' /scratch/stefan/7921156/working/building/REAL250005052573 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052573 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052573/0 /scratch/stefan/7921156/working/building/REAL250005052573 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/720 `/scratch/stefan/7921156/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](O)C2) `REAL250005052573.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052573 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](O)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [81, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 82, 110, 110, 110, 201, 201, 201, 201, 201, 201, 201, 82, 82, 82, 82, 31, 31, 9, 1, 110, 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]) total number of confs: 1153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052573 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](O)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [32, 6, 32, 117, 190, 190, 190, 201, 201, 201, 201, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 117, 117, 190, 201, 6, 1, 1, 3, 1, 1] 603 rigid atoms, others: [32, 33, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 708 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052573 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052573 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052573/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052573 Building REAL250005052574 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052574' /scratch/stefan/7921156/working/building/REAL250005052574 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052574 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052574/0 /scratch/stefan/7921156/working/building/REAL250005052574 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/721 `/scratch/stefan/7921156/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C12CC(C1)CO2) `REAL250005052574.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052574 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C12CC(C1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [81, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 82, 114, 114, 114, 146, 146, 146, 146, 146, 82, 82, 82, 82, 34, 34, 10, 1, 114, 146, 146, 146, 146, 146, 146, 146] 146 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: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052574 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C12CC(C1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [34, 10, 34, 96, 139, 139, 139, 146, 146, 146, 146, 146, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 96, 96, 139, 146, 10, 1, 1, 1, 1, 1, 1, 1] 146 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 523 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052574 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052574 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052574/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052574 Building REAL250005052575 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052575' /scratch/stefan/7921156/working/building/REAL250005052575 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052575 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052575/0 /scratch/stefan/7921156/working/building/REAL250005052575 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/722 `/scratch/stefan/7921156/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052575.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052575 none CCC=CC=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 148, 148, 135, 135, 65, 65, 65, 46, 16, 46, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 148, 148, 135, 135, 65, 46, 46, 46, 46, 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: 828 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052575 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052575 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052575/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052575 Building REAL250005052576 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052576' /scratch/stefan/7921156/working/building/REAL250005052576 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052576 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052576/0 /scratch/stefan/7921156/working/building/REAL250005052576 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/723 `/scratch/stefan/7921156/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(C)C(N)=O) `REAL250005052576.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052576 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(C)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.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [35, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 57, 57, 57, 79, 91, 91, 98, 98, 35, 35, 35, 35, 12, 12, 4, 1, 57, 79, 79, 91, 91, 91, 98, 98] 98 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: 395 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052576 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052576 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052576/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052576 Building REAL250005052577 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052577' /scratch/stefan/7921156/working/building/REAL250005052577 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052577 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052577/0 /scratch/stefan/7921156/working/building/REAL250005052577 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/724 `/scratch/stefan/7921156/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NNC(=O)[N-]1) `REAL250005052577.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052577 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', '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, 1, 11, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 6, 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: [39, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 39, 54, 54, 54, 84, 84, 84, 84, 84, 39, 39, 39, 39, 22, 22, 7, 1, 54, 84] 84 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]) 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: REAL250005052577 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', '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, 1, 11, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 6, 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: [31, 12, 31, 61, 78, 78, 78, 84, 84, 84, 84, 84, 12, 1, 12, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 61, 61, 78, 84, 12, 1] 84 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 335 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052577 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052577 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052577/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052577 Building REAL250005052578 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052578' /scratch/stefan/7921156/working/building/REAL250005052578 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052578 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052578/0 /scratch/stefan/7921156/working/building/REAL250005052578 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/725 `/scratch/stefan/7921156/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(F)CC1) `REAL250005052578.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052578 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 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, 3, 7, 3, 4, 7, 6, 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: [71, 29, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 72, 113, 113, 113, 171, 171, 171, 72, 72, 72, 72, 29, 29, 8, 1, 113, 171, 171, 171, 171] 171 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: 606 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052578 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 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, 3, 7, 3, 4, 7, 6, 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: [48, 12, 48, 122, 168, 168, 168, 171, 171, 171, 171, 171, 12, 1, 12, 1, 1, 1, 1, 48, 48, 48, 48, 122, 122, 168, 171, 12, 1, 1, 1, 1] 171 rigid atoms, others: [13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 639 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052578 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052578 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052578/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052578 Building REAL250005052579 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052579' /scratch/stefan/7921156/working/building/REAL250005052579 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052579 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052579/0 /scratch/stefan/7921156/working/building/REAL250005052579 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/726 `/scratch/stefan/7921156/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(O)C1CC1) `REAL250005052579.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052579 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 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: [79, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 81, 143, 143, 143, 186, 185, 186, 201, 201, 81, 81, 81, 81, 26, 26, 7, 1, 143, 186, 186, 186, 558, 201, 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: 1376 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: REAL250005052579 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 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: [80, 30, 80, 157, 201, 201, 201, 201, 201, 201, 201, 201, 30, 11, 30, 1, 11, 11, 1, 1, 1, 80, 80, 80, 80, 157, 157, 201, 201, 30, 11, 11, 11, 33, 1, 1, 1, 1, 1] 603 rigid atoms, others: [34, 35, 36, 37, 38, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 833 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052579 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052579 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052579/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052579 Building REAL250005052580 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052580' /scratch/stefan/7921156/working/building/REAL250005052580 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052580 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052580/0 /scratch/stefan/7921156/working/building/REAL250005052580 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/727 `/scratch/stefan/7921156/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005052580.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052580 none CC1=NC=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 52, 90, 90, 90, 92, 92, 92, 92, 92, 1, 2, 2, 2, 1, 5, 19, 19, 19, 19, 52, 52, 90, 92] 92 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 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: REAL250005052580 none CC1=NC=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 92, 86, 86, 86, 54, 24, 54, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 86, 54, 54, 54, 54, 24, 24, 8, 1] 92 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: 329 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052580 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052580 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052580/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052580 Building REAL250005052581 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052581' /scratch/stefan/7921156/working/building/REAL250005052581 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052581 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052581/0 /scratch/stefan/7921156/working/building/REAL250005052581 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/728 `/scratch/stefan/7921156/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052581.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052581 none COC(C)(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 121, 200, 200, 121, 121, 75, 27, 73, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 200, 200, 200, 200, 200, 121, 75, 75, 75, 75, 27, 27, 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: 838 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052581 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052581 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052581/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052581 Building REAL250005052582 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052582' /scratch/stefan/7921156/working/building/REAL250005052582 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052582 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052582/0 /scratch/stefan/7921156/working/building/REAL250005052582 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/729 `/scratch/stefan/7921156/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)CC#N) `REAL250005052582.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052582 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 8, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 16, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 49, 86, 86, 86, 167, 167, 201, 201, 49, 49, 49, 49, 16, 16, 6, 1, 86, 167, 167, 167, 167, 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: 874 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052582 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052582 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052582/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052582 Building REAL250005052583 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052583' /scratch/stefan/7921156/working/building/REAL250005052583 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052583 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052583/0 /scratch/stefan/7921156/working/building/REAL250005052583 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/730 `/scratch/stefan/7921156/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052583.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052583 none CCC1CC1C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 10, 10, 10, 33, 33, 103, 164, 164, 164, 175, 175, 175, 175, 175, 2, 2, 2, 2, 2, 1, 1, 1, 1, 10, 33, 33, 33, 33, 103, 103, 164, 175] 175 rigid atoms, others: [1, 2, 3, 4, 5, 25, 26, 27, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 632 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052583 none CCC1CC1C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 175, 137, 137, 137, 84, 34, 82, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 175, 175, 175, 175, 137, 84, 84, 84, 84, 34, 34, 9, 1] 175 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: 651 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052583 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052583 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052583/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052583 Building REAL250005052584 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052584' /scratch/stefan/7921156/working/building/REAL250005052584 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052584 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052584/0 /scratch/stefan/7921156/working/building/REAL250005052584 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/731 `/scratch/stefan/7921156/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)C(C)(C)O) `REAL250005052584.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052584 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 66, 66, 66, 76, 73, 76, 35, 35, 35, 35, 13, 13, 6, 1, 50, 66, 66, 66, 76, 76, 76, 76, 76, 76, 228] 228 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: 566 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052584 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052584 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052584/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052584 Building REAL250005052585 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052585' /scratch/stefan/7921156/working/building/REAL250005052585 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052585 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052585/0 /scratch/stefan/7921156/working/building/REAL250005052585 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/732 `/scratch/stefan/7921156/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=O)O1) `REAL250005052585.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052585 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=O)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 1, 11, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 5, 3, 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: [74, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 76, 110, 110, 110, 157, 157, 157, 157, 157, 76, 76, 76, 76, 28, 28, 10, 1, 110, 157, 157, 157] 157 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]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052585 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=O)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 1, 11, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 5, 3, 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: [36, 10, 36, 104, 146, 146, 146, 157, 157, 157, 157, 157, 10, 1, 10, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 104, 104, 146, 157, 10, 1, 1, 1] 157 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 569 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052585 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052585 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052585/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052585 Building REAL250005052586 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052586' /scratch/stefan/7921156/working/building/REAL250005052586 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052586 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052586/0 /scratch/stefan/7921156/working/building/REAL250005052586 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/733 `/scratch/stefan/7921156/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C12CC(C1)OC2) `REAL250005052586.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052586 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C12CC(C1)OC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 59, 69, 69, 69, 201, 201, 201, 201, 201, 59, 59, 59, 59, 24, 24, 9, 1, 69, 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]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052586 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C12CC(C1)OC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 6, 37, 115, 192, 192, 192, 201, 201, 201, 201, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 115, 115, 192, 201, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 701 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052586 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052586 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052586/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052586 Building REAL250005052587 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052587' /scratch/stefan/7921156/working/building/REAL250005052587 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052587 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052587/0 /scratch/stefan/7921156/working/building/REAL250005052587 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/734 `/scratch/stefan/7921156/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C1CC1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052587.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052587 none CC(O)C1CC1C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 2, 1, 1, 1, 1, 6, 6, 6, 20, 20, 58, 86, 86, 86, 88, 88, 88, 88, 88, 2, 2, 2, 2, 6, 1, 1, 1, 1, 6, 20, 20, 20, 20, 58, 58, 86, 88] 264 rigid atoms, others: [1, 3, 4, 5, 6, 26, 27, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 338 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052587 none CC(O)C1CC1C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [88, 88, 88, 88, 88, 68, 68, 68, 46, 17, 45, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 264, 88, 88, 88, 88, 68, 46, 46, 46, 46, 17, 17, 7, 1] 264 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 587 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052587 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052587 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052587/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052587 Building REAL250005052588 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052588' /scratch/stefan/7921156/working/building/REAL250005052588 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052588 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052588/0 /scratch/stefan/7921156/working/building/REAL250005052588 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/735 `/scratch/stefan/7921156/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](C)C2) `REAL250005052588.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052588 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](C)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 71, 102, 102, 102, 201, 201, 201, 201, 201, 201, 201, 71, 71, 71, 71, 26, 26, 8, 1, 102, 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]) total number of confs: 517 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052588 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](C)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [34, 6, 34, 114, 192, 192, 192, 201, 201, 201, 201, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 114, 114, 192, 201, 6, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 33, 37, 38, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 722 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052588 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052588 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052588/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052588 Building REAL250005052589 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052589' /scratch/stefan/7921156/working/building/REAL250005052589 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052589 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052589/0 /scratch/stefan/7921156/working/building/REAL250005052589 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/736 `/scratch/stefan/7921156/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=N1) `REAL250005052589.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052589 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 1, 8, 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, 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] 0 hydrogens 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, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 59, 87, 87, 87, 165, 201, 201, 201, 201, 59, 59, 59, 59, 25, 25, 8, 1, 87, 165, 165, 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: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052589 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 1, 8, 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, 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] 0 hydrogens 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, 47, 88, 163, 196, 196, 196, 201, 201, 201, 201, 201, 47, 9, 47, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 163, 163, 196, 201, 47, 9, 9, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 798 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052589 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052589 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052589/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052589 Building REAL250005052590 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052590' /scratch/stefan/7921156/working/building/REAL250005052590 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052590 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052590/0 /scratch/stefan/7921156/working/building/REAL250005052590 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/737 `/scratch/stefan/7921156/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)C[NH+](C)C) `REAL250005052590.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052590 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 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: [24, 15, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 30, 30, 30, 37, 37, 37, 37, 37, 37, 24, 24, 24, 24, 15, 15, 8, 1, 30, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 37 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, 42]) total number of confs: 171 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052590 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052590 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052590/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052590 Building REAL250005052591 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052591' /scratch/stefan/7921156/working/building/REAL250005052591 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052591 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052591/0 /scratch/stefan/7921156/working/building/REAL250005052591 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/738 `/scratch/stefan/7921156/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052591.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052591 none C=CC(C)(O)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 113, 201, 201, 113, 113, 71, 25, 71, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 113, 71, 71, 71, 71, 25, 25, 8, 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: 1431 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052591 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052591 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052591/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052591 Building REAL250005052592 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052592' /scratch/stefan/7921156/working/building/REAL250005052592 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052592 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052592/0 /scratch/stefan/7921156/working/building/REAL250005052592 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/739 `/scratch/stefan/7921156/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CO)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052592.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052592 none CCC(C)(CO)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [174, 145, 93, 145, 145, 197, 93, 93, 55, 23, 55, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 183, 183, 183, 183, 183, 145, 145, 145, 197, 197, 591, 93, 55, 55, 55, 55, 23, 23, 9, 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: 1722 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052592 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052592 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052592/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052592 Building REAL250005052593 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052593' /scratch/stefan/7921156/working/building/REAL250005052593 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052593 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052593/0 /scratch/stefan/7921156/working/building/REAL250005052593 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/740 `/scratch/stefan/7921156/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1([NH+](C)C)CC1) `REAL250005052593.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052593 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1([NH+](C)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.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 6 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: 17 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: REAL250005052593 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1([NH+](C)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.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 4, 4, 4, 1, 1, 4, 4, 4, 4, 4, 4, 4, 6, 3, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 6 rigid atoms, others: [37, 38, 39, 40, 13, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 28 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052593 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052593/1 /scratch/stefan/7921156/working/building/REAL250005052593 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/741 `/scratch/stefan/7921156/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(N(C)C)CC1) `REAL250005052593.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052593/1/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: REAL250005052593 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(N(C)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.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [36, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 36, 46, 46, 46, 63, 63, 63, 63, 63, 36, 36, 36, 36, 19, 19, 7, 1, 46, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63] 63 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: 239 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: REAL250005052593 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(N(C)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.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 37, 59, 59, 59, 63, 63, 63, 63, 63, 6, 1, 6, 1, 1, 4, 4, 1, 1, 15, 15, 15, 15, 37, 37, 59, 63, 6, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 63 rigid atoms, others: [36, 37, 38, 39, 13, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 225 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052593 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052593 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052593/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052593/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052593 Building REAL250005052594 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052594' /scratch/stefan/7921156/working/building/REAL250005052594 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052594 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052594/0 /scratch/stefan/7921156/working/building/REAL250005052594 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/742 `/scratch/stefan/7921156/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052594.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052594 none CCCC=CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 166, 114, 114, 46, 46, 46, 30, 13, 30, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 166, 166, 114, 114, 46, 30, 30, 30, 30, 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: 875 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052594 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052594 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052594/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052594 Building REAL250005052595 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052595' /scratch/stefan/7921156/working/building/REAL250005052595 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052595 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052595/0 /scratch/stefan/7921156/working/building/REAL250005052595 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/743 `/scratch/stefan/7921156/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052595.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052595 none CC=C(F)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 87, 101, 87, 87, 67, 28, 66, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 87, 67, 67, 67, 67, 28, 28, 10, 1] 101 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: 391 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052595 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052595 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052595/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052595 Building REAL250005052596 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052596' /scratch/stefan/7921156/working/building/REAL250005052596 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052596 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052596/0 /scratch/stefan/7921156/working/building/REAL250005052596 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/744 `/scratch/stefan/7921156/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005052596.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052596 none CCC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [173, 171, 101, 101, 101, 70, 29, 70, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 171, 196, 192, 183, 183, 183, 183, 183, 171, 101, 70, 70, 70, 70, 29, 29, 9, 1, 196, 196, 196, 196, 196, 196, 196] 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: 1023 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052596 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052596 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052596/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052596 Building REAL250005052597 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052597' /scratch/stefan/7921156/working/building/REAL250005052597 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052597 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052597/0 /scratch/stefan/7921156/working/building/REAL250005052597 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/745 `/scratch/stefan/7921156/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H](C)[NH+](C)C) `REAL250005052597.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052597 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 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, 7, 7, 3, 7, 3, 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] 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, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 6 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]) total number of confs: 13 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052597 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052597/1 /scratch/stefan/7921156/working/building/REAL250005052597 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/746 `/scratch/stefan/7921156/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H](C)N(C)C) `REAL250005052597.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052597/1/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: REAL250005052597 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 10, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [63, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 63, 98, 98, 98, 136, 136, 136, 141, 141, 63, 63, 63, 63, 30, 30, 11, 1, 98, 136, 136, 136, 141, 141, 141, 141, 141, 141] 141 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: 583 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052597 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052597 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052597/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052597/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052597 Building REAL250005052598 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052598' /scratch/stefan/7921156/working/building/REAL250005052598 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052598 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052598/0 /scratch/stefan/7921156/working/building/REAL250005052598 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/747 `/scratch/stefan/7921156/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CO)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052598.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052598 none CC(C)C(CO)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [151, 131, 149, 71, 131, 166, 71, 71, 45, 20, 45, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 151, 151, 131, 166, 166, 498, 71, 45, 45, 45, 45, 20, 20, 9, 1] 510 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1375 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052598 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052598 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052598/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052598 Building REAL250005052599 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052599' /scratch/stefan/7921156/working/building/REAL250005052599 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052599 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052599/0 /scratch/stefan/7921156/working/building/REAL250005052599 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/748 `/scratch/stefan/7921156/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052599.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052599 none CCOC=CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 134, 134, 56, 56, 56, 44, 16, 44, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 134, 134, 56, 44, 44, 44, 44, 16, 16, 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: 593 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052599 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052599 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052599/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052599 Building REAL250005052600 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052600' /scratch/stefan/7921156/working/building/REAL250005052600 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005052600 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052600/0 /scratch/stefan/7921156/working/building/REAL250005052600 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/749 `/scratch/stefan/7921156/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052600.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052600 none CCN1CCC1C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 28, 85, 167, 167, 167, 193, 193, 193, 193, 193, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 85, 85, 167, 193] 200 rigid atoms, others: [1, 2, 3, 4, 5, 6, 26, 27, 28, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 623 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: REAL250005052600 none CCN1CCC1C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 193, 193, 193, 193, 152, 152, 152, 98, 38, 96, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 193, 193, 193, 193, 193, 152, 98, 98, 98, 98, 38, 38, 10, 1] 200 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: 755 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052600 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052600/1 /scratch/stefan/7921156/working/building/REAL250005052600 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/750 `/scratch/stefan/7921156/working/3D/750' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+]1CCC1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052600.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052600/1/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: REAL250005052600 none CC[N@@H+]1CCC1C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 20, 20, 20, 20, 27, 27, 27, 27, 27, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 20, 20, 20, 27] 29 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 27, 28, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 103 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: REAL250005052600 none CC[N@@H+]1CCC1C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 27, 27, 27, 27, 27, 24, 24, 24, 17, 12, 17, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 27, 27, 27, 27, 27, 24, 17, 17, 17, 17, 12, 12, 9, 1] 29 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: 107 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052600 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `2' /scratch/stefan/7921156/working/building/REAL250005052600/2 /scratch/stefan/7921156/working/building/REAL250005052600 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 2 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/751 `/scratch/stefan/7921156/working/3D/751' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+]1CCC1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052600.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005052600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052600/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052600 none CC[N@H+]1CCC1C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 9, 9, 9, 9, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 9, 9, 9, 10] 10 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 27, 28, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052600 none CC[N@H+]1CCC1C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 9, 9, 9, 9, 8, 9, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 8, 8, 6, 1] 10 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052600 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052600 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052600/0.* 2: /scratch/stefan/7921156/working/building/REAL250005052600/2.* 1: /scratch/stefan/7921156/working/building/REAL250005052600/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052600 Building REAL250005052601 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052601' /scratch/stefan/7921156/working/building/REAL250005052601 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052601 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052601/0 /scratch/stefan/7921156/working/building/REAL250005052601 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/752 `/scratch/stefan/7921156/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=C(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052601.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052601 none CCC(C)=C(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 145, 145, 145, 100, 145, 100, 100, 58, 20, 57, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 145, 145, 145, 145, 145, 145, 100, 58, 58, 58, 58, 20, 20, 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: 855 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052601 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052601 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052601/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052601 Building REAL250005052602 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052602' /scratch/stefan/7921156/working/building/REAL250005052602 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052602 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052602/0 /scratch/stefan/7921156/working/building/REAL250005052602 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/753 `/scratch/stefan/7921156/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005052602.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052602 none COC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 9, 9, 9, 35, 35, 123, 190, 190, 190, 201, 201, 201, 201, 201, 1, 1, 1, 6, 6, 6, 9, 35, 35, 35, 35, 123, 123, 190, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 36, 37, 35, 33, 34, 18, 19, 20, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 716 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: REAL250005052602 none COC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 145, 145, 145, 86, 32, 84, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 145, 86, 86, 86, 86, 32, 32, 9, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 719 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052602 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052602 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052602/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052602 Building REAL250005052603 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052603' /scratch/stefan/7921156/working/building/REAL250005052603 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052603 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052603/0 /scratch/stefan/7921156/working/building/REAL250005052603 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/754 `/scratch/stefan/7921156/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052603.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052603 none C=CCCC(=O)C(=O)NC(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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 80, 56, 80, 56, 56, 33, 9, 33, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 56, 33, 33, 33, 33, 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: 813 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052603 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052603 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052603/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052603 Building REAL250005052604 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052604' /scratch/stefan/7921156/working/building/REAL250005052604 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052604 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052604/0 /scratch/stefan/7921156/working/building/REAL250005052604 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/755 `/scratch/stefan/7921156/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052604.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052604 none CC(O)CCCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [186, 152, 201, 112, 94, 32, 32, 32, 29, 15, 29, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 143, 151, 132, 132, 94, 94, 32, 29, 29, 29, 29, 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: 1744 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052604 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052604 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052604/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052604 Building REAL250005052605 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052605' /scratch/stefan/7921156/working/building/REAL250005052605 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052605 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052605/0 /scratch/stefan/7921156/working/building/REAL250005052605 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/756 `/scratch/stefan/7921156/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)OCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052605.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052605 none CC(=O)OCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 5, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 154, 94, 94, 94, 59, 20, 58, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 154, 154, 94, 59, 59, 59, 59, 20, 20, 4, 1] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 734 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052605 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052605 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052605/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052605 Building REAL250005052606 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052606' /scratch/stefan/7921156/working/building/REAL250005052606 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052606 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052606/0 /scratch/stefan/7921156/working/building/REAL250005052606 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/757 `/scratch/stefan/7921156/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052606.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052606 none CC(=O)NCCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 178, 165, 78, 78, 78, 57, 24, 57, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 178, 178, 165, 165, 78, 57, 57, 57, 57, 24, 24, 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: 837 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052606 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052606 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052606/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052606 Building REAL250005052607 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052607' /scratch/stefan/7921156/working/building/REAL250005052607 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052607 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052607/0 /scratch/stefan/7921156/working/building/REAL250005052607 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/758 `/scratch/stefan/7921156/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNC(=O)N1) `REAL250005052607.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052607 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNC(=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.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 6, 4, 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: [51, 22, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 52, 73, 73, 73, 93, 93, 93, 93, 93, 52, 52, 52, 52, 22, 22, 10, 1, 73, 93, 93, 93] 93 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]) 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: REAL250005052607 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNC(=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.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 6, 4, 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: [24, 6, 24, 57, 88, 88, 88, 93, 93, 93, 93, 93, 6, 1, 6, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 57, 57, 88, 93, 6, 1, 1, 1] 93 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052607 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052607 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052607/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052607 Building REAL250005052608 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052608' /scratch/stefan/7921156/working/building/REAL250005052608 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052608 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052608/0 /scratch/stefan/7921156/working/building/REAL250005052608 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/759 `/scratch/stefan/7921156/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)[NH+](C)C) `REAL250005052608.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052608 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 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, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 1, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 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, 42]) total number of confs: 28 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052608 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052608 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052608/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052608 Building REAL250005052609 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052609' /scratch/stefan/7921156/working/building/REAL250005052609 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052609 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052609/0 /scratch/stefan/7921156/working/building/REAL250005052609 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/760 `/scratch/stefan/7921156/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)(F)CO) `REAL250005052609.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052609 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)(F)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.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 15, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 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: [62, 21, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 63, 106, 106, 106, 197, 197, 197, 201, 63, 63, 63, 63, 21, 21, 5, 1, 106, 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]) total number of confs: 1410 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052609 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052609 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052609/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052609 Building REAL250005052610 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052610' /scratch/stefan/7921156/working/building/REAL250005052610 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052610 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052610/0 /scratch/stefan/7921156/working/building/REAL250005052610 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/761 `/scratch/stefan/7921156/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C#CC1(C)CC1) `REAL250005052610.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052610 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C#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.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [64, 27, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 64, 85, 85, 85, 85, 85, 85, 85, 85, 64, 64, 64, 64, 27, 27, 8, 1, 85, 85, 85, 85, 85, 85, 85, 85] 85 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: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052610 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C#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.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 36, 82, 82, 82, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 36, 36, 82, 85, 1, 2, 2, 2, 1, 1, 1, 1] 85 rigid atoms, others: [1, 34, 35, 36, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052610 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052610 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052610/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052610 Building REAL250005052611 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052611' /scratch/stefan/7921156/working/building/REAL250005052611 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052611 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052611/0 /scratch/stefan/7921156/working/building/REAL250005052611 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/762 `/scratch/stefan/7921156/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052611.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052611 none CC(=O)C=CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 94, 101, 94, 70, 70, 70, 47, 24, 47, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 101, 101, 101, 94, 94, 70, 47, 47, 47, 47, 24, 24, 10, 1] 101 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: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052611 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052611 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052611/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052611 Building REAL250005052612 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052612' /scratch/stefan/7921156/working/building/REAL250005052612 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052612 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052612/0 /scratch/stefan/7921156/working/building/REAL250005052612 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/763 `/scratch/stefan/7921156/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COC1CC1) `REAL250005052612.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052612 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 33, 57, 57, 57, 127, 172, 201, 201, 33, 33, 33, 33, 11, 11, 3, 1, 57, 127, 127, 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: 707 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: REAL250005052612 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 76, 122, 166, 201, 201, 201, 201, 201, 201, 201, 201, 76, 24, 76, 6, 1, 1, 1, 1, 122, 122, 122, 122, 166, 166, 201, 201, 76, 24, 24, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 805 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052612 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052612 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052612/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052612 Building REAL250005052613 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052613' /scratch/stefan/7921156/working/building/REAL250005052613 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052613 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052613/0 /scratch/stefan/7921156/working/building/REAL250005052613 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/764 `/scratch/stefan/7921156/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=CN1) `REAL250005052613.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052613 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 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: [28, 18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 31, 31, 31, 32, 32, 32, 32, 28, 28, 28, 28, 18, 18, 9, 1, 31, 32, 32, 32] 32 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052613 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 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: [16, 4, 16, 47, 90, 90, 90, 101, 101, 101, 101, 101, 4, 1, 4, 1, 1, 1, 1, 1, 16, 16, 16, 16, 47, 47, 90, 101, 4, 1, 1, 1] 101 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052613 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052613 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052613/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052613 Building REAL250005052614 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052614' /scratch/stefan/7921156/working/building/REAL250005052614 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052614 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052614/0 /scratch/stefan/7921156/working/building/REAL250005052614 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/765 `/scratch/stefan/7921156/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CC1CCC1) `REAL250005052614.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052614 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 54, 82, 82, 82, 162, 162, 201, 201, 201, 54, 54, 54, 54, 20, 20, 5, 1, 82, 162, 162, 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: 693 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052614 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 44, 92, 161, 201, 201, 201, 201, 201, 201, 201, 201, 44, 9, 44, 9, 1, 1, 1, 1, 1, 92, 92, 92, 92, 161, 161, 201, 201, 44, 9, 9, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 791 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052614 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052614 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052614/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052614 Building REAL250005052615 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052615' /scratch/stefan/7921156/working/building/REAL250005052615 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052615 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052615/0 /scratch/stefan/7921156/working/building/REAL250005052615 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/766 `/scratch/stefan/7921156/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN=CS1) `REAL250005052615.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052615 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN=CS1 NO_LONG_NAME dock atom types: ['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.2', 'N.2', 'C.2', 'S.3', 'H', 'H', '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, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [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] 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: [68, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 105, 105, 105, 113, 113, 113, 113, 69, 69, 69, 69, 31, 31, 9, 1, 105, 113] 113 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]) 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: REAL250005052615 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN=CS1 NO_LONG_NAME dock atom types: ['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.2', 'N.2', 'C.2', 'S.3', 'H', 'H', '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, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [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] 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: [22, 7, 22, 63, 109, 109, 109, 113, 113, 113, 113, 113, 7, 1, 7, 1, 1, 1, 1, 1, 22, 22, 22, 22, 63, 63, 109, 113, 7, 1] 113 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 398 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052615 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052615 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052615/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052615 Building REAL250005052616 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052616' /scratch/stefan/7921156/working/building/REAL250005052616 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052616 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052616/0 /scratch/stefan/7921156/working/building/REAL250005052616 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/767 `/scratch/stefan/7921156/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(=O)CO1) `REAL250005052616.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052616 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(=O)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.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 11, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [86, 33, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 87, 132, 132, 132, 178, 178, 178, 178, 178, 87, 87, 87, 87, 33, 33, 11, 1, 132, 178, 178, 178, 178, 178] 178 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: 647 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: REAL250005052616 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(=O)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.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 11, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [37, 11, 37, 112, 169, 169, 169, 178, 178, 178, 178, 178, 11, 1, 11, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 112, 112, 169, 178, 11, 1, 1, 1, 1, 1] 178 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 634 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052616 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052616 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052616/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052616 Building REAL250005052617 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052617' /scratch/stefan/7921156/working/building/REAL250005052617 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052617 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052617/0 /scratch/stefan/7921156/working/building/REAL250005052617 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/768 `/scratch/stefan/7921156/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052617.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052617 none CC(C)NC(=O)C(=O)NC(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, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 201, 198, 152, 198, 152, 152, 87, 30, 85, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 198, 152, 87, 87, 87, 87, 30, 30, 10, 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: 723 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052617 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052617 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052617/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052617 Building REAL250005052618 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052618' /scratch/stefan/7921156/working/building/REAL250005052618 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052618 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052618/0 /scratch/stefan/7921156/working/building/REAL250005052618 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/769 `/scratch/stefan/7921156/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005052618.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052618 none CC1=C(C(=O)NC(C)CNC(=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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 40, 40, 120, 177, 177, 177, 188, 188, 188, 188, 188, 1, 1, 1, 2, 2, 2, 9, 40, 40, 40, 40, 120, 120, 177, 188, 1, 1, 1, 1] 188 rigid atoms, others: [0, 1, 2, 3, 36, 35, 33, 34, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052618 none CC1=C(C(=O)NC(C)CNC(=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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 117, 117, 117, 74, 30, 72, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 188, 188, 117, 74, 74, 74, 74, 30, 30, 10, 1, 188, 188, 188, 188] 188 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 556 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052618 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052618 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052618/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052618 Building REAL250005052619 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052619' /scratch/stefan/7921156/working/building/REAL250005052619 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052619 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052619/0 /scratch/stefan/7921156/working/building/REAL250005052619 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/770 `/scratch/stefan/7921156/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=CN1C) `REAL250005052619.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052619 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=CN1C NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 1, 1, 8, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [80, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 81, 111, 111, 111, 113, 113, 113, 113, 113, 81, 81, 81, 81, 32, 32, 9, 1, 111, 113, 113, 113, 113, 113] 113 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: 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: REAL250005052619 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=CN1C NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 1, 1, 8, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [17, 3, 17, 55, 106, 106, 106, 113, 113, 113, 113, 113, 3, 1, 3, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 55, 55, 106, 113, 3, 1, 1, 2, 2, 2] 113 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 395 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052619 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052619 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052619/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052619 Building REAL250005052620 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052620' /scratch/stefan/7921156/working/building/REAL250005052620 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052620 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052620/0 /scratch/stefan/7921156/working/building/REAL250005052620 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/771 `/scratch/stefan/7921156/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)CO) `REAL250005052620.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052620 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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', '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, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [69, 23, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 71, 109, 109, 109, 192, 192, 201, 71, 71, 71, 71, 23, 23, 7, 1, 109, 192, 192, 192, 192, 201, 201, 603] 603 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: 1455 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052620 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052620 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052620/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052620 Building REAL250005052621 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052621' /scratch/stefan/7921156/working/building/REAL250005052621 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052621 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052621/0 /scratch/stefan/7921156/working/building/REAL250005052621 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/772 `/scratch/stefan/7921156/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CON=C1) `REAL250005052621.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052621 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 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: [50, 21, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 51, 78, 78, 78, 135, 135, 135, 135, 51, 51, 51, 51, 21, 21, 10, 1, 78, 135, 135] 135 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]) total number of confs: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052621 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 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: [21, 5, 21, 78, 125, 125, 125, 135, 135, 135, 135, 135, 5, 1, 5, 1, 1, 1, 1, 1, 21, 21, 21, 21, 78, 78, 125, 135, 5, 1, 1] 135 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 487 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052621 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052621 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052621/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052621 Building REAL250005052622 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052622' /scratch/stefan/7921156/working/building/REAL250005052622 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052622 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052622/0 /scratch/stefan/7921156/working/building/REAL250005052622 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/773 `/scratch/stefan/7921156/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCCO) `REAL250005052622.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052622 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [38, 18, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 38, 47, 47, 47, 142, 173, 198, 200, 38, 38, 38, 38, 18, 18, 5, 1, 47, 142, 142, 185, 185, 197, 199, 201, 201, 600] 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, 36, 37]) total number of confs: 1555 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052622 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052622 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052622/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052622 Building REAL250005052623 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052623' /scratch/stefan/7921156/working/building/REAL250005052623 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052623 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052623/0 /scratch/stefan/7921156/working/building/REAL250005052623 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/774 `/scratch/stefan/7921156/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(=O)C1CC1) `REAL250005052623.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052623 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 11, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 54, 94, 94, 94, 152, 152, 201, 201, 54, 54, 54, 54, 15, 15, 4, 1, 94, 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]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052623 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 11, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 48, 89, 152, 201, 201, 201, 201, 201, 201, 201, 201, 48, 12, 48, 1, 12, 1, 1, 1, 89, 89, 89, 89, 152, 152, 201, 201, 48, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 15, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 779 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052623 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052623 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052623/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052623 Building REAL250005052624 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052624' /scratch/stefan/7921156/working/building/REAL250005052624 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052624 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052624/0 /scratch/stefan/7921156/working/building/REAL250005052624 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/775 `/scratch/stefan/7921156/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1COC(=O)N1) `REAL250005052624.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052624 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1COC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [67, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 67, 103, 103, 103, 123, 123, 123, 123, 123, 123, 67, 67, 67, 67, 25, 25, 8, 1, 103, 123, 123, 123] 123 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]) total number of confs: 445 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052624 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1COC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [31, 10, 31, 90, 114, 114, 114, 123, 123, 123, 123, 123, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 90, 90, 114, 123, 10, 1, 1, 1] 123 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 458 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052624 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052624 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052624/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052624 Building REAL250005052625 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052625' /scratch/stefan/7921156/working/building/REAL250005052625 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052625 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052625/0 /scratch/stefan/7921156/working/building/REAL250005052625 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/776 `/scratch/stefan/7921156/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(O)CC1) `REAL250005052625.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052625 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 525 conformations in input total number of sets (complete confs): 525 using faster count positions algorithm for large data unique positions, atoms: [64, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 64, 92, 92, 92, 158, 175, 175, 175, 64, 64, 64, 64, 23, 23, 8, 1, 92, 158, 158, 525, 175, 175, 175, 175] 525 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: 1243 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052625 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 525 conformations in input total number of sets (complete confs): 525 using faster count positions algorithm for large data unique positions, atoms: [71, 29, 71, 135, 170, 170, 170, 175, 175, 175, 175, 175, 29, 7, 29, 1, 1, 1, 1, 1, 71, 71, 71, 71, 135, 135, 170, 175, 29, 7, 7, 6, 1, 1, 1, 1] 525 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 703 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052625 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052625 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052625/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052625 Building REAL250005052626 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052626' /scratch/stefan/7921156/working/building/REAL250005052626 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052626 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052626/0 /scratch/stefan/7921156/working/building/REAL250005052626 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/777 `/scratch/stefan/7921156/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC1F) `REAL250005052626.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052626 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [83, 33, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 84, 122, 122, 122, 200, 200, 200, 200, 84, 84, 84, 84, 33, 33, 11, 1, 122, 200, 200, 200, 200, 200, 200] 200 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: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052626 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [45, 11, 45, 129, 189, 189, 189, 200, 200, 200, 200, 200, 11, 1, 11, 1, 1, 1, 1, 1, 45, 45, 45, 45, 129, 129, 189, 200, 11, 1, 1, 1, 1, 1, 1] 200 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 715 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052626 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052626 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052626/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052626 Building REAL250005052627 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052627' /scratch/stefan/7921156/working/building/REAL250005052627 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052627 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052627/0 /scratch/stefan/7921156/working/building/REAL250005052627 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/778 `/scratch/stefan/7921156/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)C1CCC1) `REAL250005052627.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052627 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)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.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [60, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 62, 111, 111, 111, 151, 151, 201, 201, 201, 62, 62, 62, 62, 19, 19, 5, 1, 111, 151, 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]) total number of confs: 797 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: REAL250005052627 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)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.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 33, 78, 157, 201, 201, 201, 201, 201, 201, 201, 201, 33, 6, 33, 1, 6, 1, 1, 1, 1, 78, 78, 78, 78, 157, 157, 201, 201, 33, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 796 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052627 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052627 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052627/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052627 Building REAL250005052628 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052628' /scratch/stefan/7921156/working/building/REAL250005052628 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052628 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052628/0 /scratch/stefan/7921156/working/building/REAL250005052628 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/779 `/scratch/stefan/7921156/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(C)O1) `REAL250005052628.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052628 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(C)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 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, 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: [82, 36, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 84, 130, 130, 130, 147, 147, 147, 147, 147, 84, 84, 84, 84, 36, 36, 10, 1, 130, 147, 147, 147, 147, 147, 147, 147, 147, 147] 147 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: 535 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052628 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(C)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 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, 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: [33, 10, 33, 92, 132, 132, 132, 147, 147, 147, 147, 147, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 92, 92, 132, 147, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2] 147 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 533 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052628 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052628 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052628/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052628 Building REAL250005052629 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052629' /scratch/stefan/7921156/working/building/REAL250005052629 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052629 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052629/0 /scratch/stefan/7921156/working/building/REAL250005052629 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/780 `/scratch/stefan/7921156/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1CF) `REAL250005052629.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052629 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 64, 94, 94, 94, 195, 195, 195, 195, 195, 201, 64, 64, 64, 64, 23, 23, 9, 1, 94, 195, 195, 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]) total number of confs: 657 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052629 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 12, 38, 108, 173, 173, 173, 195, 195, 195, 195, 195, 12, 1, 12, 1, 1, 1, 1, 1, 1, 9, 38, 38, 38, 38, 108, 108, 173, 195, 12, 1, 1, 9, 9] 201 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 704 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052629 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052629 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052629/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052629 Building REAL250005052630 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052630' /scratch/stefan/7921156/working/building/REAL250005052630 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052630 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052630/0 /scratch/stefan/7921156/working/building/REAL250005052630 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/781 `/scratch/stefan/7921156/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)=C1CCC1) `REAL250005052630.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052630 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)=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.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 15, 1, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [78, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 79, 119, 119, 119, 143, 143, 143, 143, 143, 79, 79, 79, 79, 33, 33, 9, 1, 119, 143, 143, 143, 143, 143, 143] 143 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: 523 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: REAL250005052630 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)=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.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 15, 1, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [30, 9, 30, 80, 132, 132, 132, 143, 143, 143, 143, 143, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 80, 80, 132, 143, 9, 1, 1, 1, 1, 1, 1] 143 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 504 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052630 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052630 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052630/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052630 Building REAL250005052631 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052631' /scratch/stefan/7921156/working/building/REAL250005052631 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052631 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052631/0 /scratch/stefan/7921156/working/building/REAL250005052631 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/782 `/scratch/stefan/7921156/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CO)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052631.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052631 none CCC(CO)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [180, 149, 72, 149, 196, 72, 72, 41, 16, 41, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 185, 185, 185, 185, 185, 149, 196, 196, 588, 72, 41, 41, 41, 41, 16, 16, 5, 1] 603 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1687 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052631 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052631 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052631/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052631 Building REAL250005052632 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052632' /scratch/stefan/7921156/working/building/REAL250005052632 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052632 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052632/0 /scratch/stefan/7921156/working/building/REAL250005052632 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/783 `/scratch/stefan/7921156/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(O)C1CC1) `REAL250005052632.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052632 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7] 1 hydrogens need rotated 561 conformations in input total number of sets (complete confs): 561 using faster count positions algorithm for large data unique positions, atoms: [31, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 31, 56, 56, 56, 134, 160, 159, 187, 187, 31, 31, 31, 31, 14, 14, 5, 1, 56, 134, 134, 160, 480, 187, 187, 187, 187, 187] 561 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: 1269 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: REAL250005052632 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7] 1 hydrogens need rotated 561 conformations in input total number of sets (complete confs): 561 using faster count positions algorithm for large data unique positions, atoms: [124, 80, 124, 175, 186, 186, 186, 187, 187, 187, 187, 187, 80, 24, 80, 6, 1, 6, 1, 1, 1, 124, 124, 124, 124, 175, 175, 186, 187, 80, 24, 24, 6, 18, 1, 1, 1, 1, 1] 561 rigid atoms, others: [34, 35, 36, 37, 38, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 779 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052632 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052632 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052632/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052632 Building REAL250005052633 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052633' /scratch/stefan/7921156/working/building/REAL250005052633 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052633 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052633/0 /scratch/stefan/7921156/working/building/REAL250005052633 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/784 `/scratch/stefan/7921156/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC1CC1)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052633.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052633 none CC(=CC1CC1)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 6, 30, 30, 30, 73, 73, 148, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 30, 73, 73, 73, 73, 148, 148, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 25, 26, 27, 28, 29] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 762 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: REAL250005052633 none CC(=CC1CC1)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 65, 139, 139, 201, 201, 65, 65, 46, 16, 46, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 201, 201, 201, 201, 201, 65, 46, 46, 46, 46, 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: 708 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052633 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052633 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052633/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052633 Building REAL250005052634 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052634' /scratch/stefan/7921156/working/building/REAL250005052634 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052634 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052634/0 /scratch/stefan/7921156/working/building/REAL250005052634 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/785 `/scratch/stefan/7921156/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@@H]1C#N) `REAL250005052634.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052634 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [49, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 50, 76, 76, 76, 85, 85, 85, 85, 85, 85, 50, 50, 50, 50, 20, 20, 9, 1, 76, 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]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052634 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 23, 56, 78, 78, 78, 85, 85, 85, 85, 85, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 56, 56, 78, 85, 8, 1, 1] 85 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052634 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052634 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052634/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052634 Building REAL250005052635 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052635' /scratch/stefan/7921156/working/building/REAL250005052635 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052635 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052635/0 /scratch/stefan/7921156/working/building/REAL250005052635 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/786 `/scratch/stefan/7921156/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CN=CO1) `REAL250005052635.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052635 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 8, 1, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 37, 54, 54, 54, 123, 201, 201, 201, 201, 37, 37, 37, 37, 15, 15, 4, 1, 54, 123, 123, 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: 617 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052635 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 8, 1, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 34, 73, 150, 201, 201, 201, 201, 201, 201, 201, 201, 34, 5, 34, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 150, 150, 201, 201, 34, 5, 5, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 804 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052635 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052635 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052635/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052635 Building REAL250005052636 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052636' /scratch/stefan/7921156/working/building/REAL250005052636 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052636 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052636/0 /scratch/stefan/7921156/working/building/REAL250005052636 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/787 `/scratch/stefan/7921156/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COCC1) `REAL250005052636.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052636 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 5, 5, 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, 7, 3, 7, 3, 4, 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 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [67, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 69, 102, 102, 102, 132, 132, 132, 132, 69, 69, 69, 69, 28, 28, 10, 1, 102, 132, 132, 132, 132, 132] 132 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: 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: REAL250005052636 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 5, 5, 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, 7, 3, 7, 3, 4, 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 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [38, 11, 38, 95, 127, 127, 127, 132, 132, 132, 132, 132, 11, 1, 11, 1, 1, 1, 1, 1, 38, 38, 38, 38, 95, 95, 127, 132, 11, 1, 1, 1, 1, 1] 132 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 503 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052636 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052636 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052636/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052636 Building REAL250005052637 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052637' /scratch/stefan/7921156/working/building/REAL250005052637 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052637 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052637/0 /scratch/stefan/7921156/working/building/REAL250005052637 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/788 `/scratch/stefan/7921156/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC(C)(C)O) `REAL250005052637.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052637 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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, 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: [45, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 65, 65, 65, 164, 165, 201, 201, 200, 45, 45, 45, 45, 16, 16, 4, 1, 65, 164, 164, 166, 166, 201, 201, 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: 1493 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052637 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052637 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052637/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052637 Building REAL250005052638 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052638' /scratch/stefan/7921156/working/building/REAL250005052638 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052638 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052638/0 /scratch/stefan/7921156/working/building/REAL250005052638 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/789 `/scratch/stefan/7921156/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005052638.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052638 none CC1=CC=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 62, 96, 96, 96, 103, 103, 103, 103, 103, 1, 2, 2, 2, 1, 1, 7, 21, 21, 21, 21, 62, 62, 96, 103, 1] 103 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 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: REAL250005052638 none CC1=CC=C(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 87, 87, 87, 64, 24, 63, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 103, 87, 64, 64, 64, 64, 24, 24, 9, 1, 103] 103 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 359 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052638 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052638 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052638/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052638 Building REAL250005052639 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052639' /scratch/stefan/7921156/working/building/REAL250005052639 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052639 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052639/0 /scratch/stefan/7921156/working/building/REAL250005052639 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/790 `/scratch/stefan/7921156/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CC1) `REAL250005052639.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052639 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 441 conformations in input total number of sets (complete confs): 441 using faster count positions algorithm for large data unique positions, atoms: [76, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 78, 112, 112, 112, 147, 147, 147, 78, 78, 78, 78, 32, 32, 10, 1, 112, 441, 147, 147, 147, 147] 441 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]) total number of confs: 983 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052639 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 441 conformations in input total number of sets (complete confs): 441 using faster count positions algorithm for large data unique positions, atoms: [38, 11, 38, 99, 138, 138, 138, 147, 147, 147, 147, 147, 11, 1, 11, 1, 1, 1, 1, 38, 38, 38, 38, 99, 99, 138, 147, 11, 6, 1, 1, 1, 1] 441 rigid atoms, others: [32, 13, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 542 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052639 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052639 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052639/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052639 Building REAL250005052640 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052640' /scratch/stefan/7921156/working/building/REAL250005052640 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052640 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052640/0 /scratch/stefan/7921156/working/building/REAL250005052640 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/791 `/scratch/stefan/7921156/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCC1) `REAL250005052640.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052640 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [48, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 48, 58, 58, 58, 58, 58, 58, 48, 48, 48, 48, 21, 21, 9, 1, 58, 58, 58, 58, 58, 58] 58 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]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052640 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 40, 56, 56, 56, 58, 58, 58, 58, 58, 5, 1, 5, 1, 1, 1, 1, 14, 14, 14, 14, 40, 40, 56, 58, 5, 1, 1, 1, 1, 1] 58 rigid atoms, others: [32, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052640 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052640 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052640/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052640 Building REAL250005052641 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052641' /scratch/stefan/7921156/working/building/REAL250005052641 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052641 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052641/0 /scratch/stefan/7921156/working/building/REAL250005052641 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/792 `/scratch/stefan/7921156/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NOC(C)C1) `REAL250005052641.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052641 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NOC(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.2', 'O.2', 'C.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 12, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [85, 36, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 87, 126, 126, 126, 137, 137, 137, 137, 137, 87, 87, 87, 87, 36, 36, 12, 1, 126, 137, 137, 137, 137, 137, 137] 137 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: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052641 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NOC(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.2', 'O.2', 'C.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 12, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [33, 13, 33, 91, 130, 130, 130, 137, 137, 137, 137, 137, 13, 1, 13, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 91, 91, 130, 137, 13, 1, 2, 2, 2, 1, 1] 137 rigid atoms, others: [34, 35, 13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 504 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052641 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052641 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052641/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052641 Building REAL250005052642 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052642' /scratch/stefan/7921156/working/building/REAL250005052642 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052642 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052642/0 /scratch/stefan/7921156/working/building/REAL250005052642 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/793 `/scratch/stefan/7921156/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)CF) `REAL250005052642.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052642 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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', '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, 8, 1, 11, 5, 5, 5, 15, 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, 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] 0 hydrogens 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, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 67, 113, 113, 113, 197, 197, 201, 67, 67, 67, 67, 22, 22, 7, 1, 113, 197, 197, 197, 197, 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: 828 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052642 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052642 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052642/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052642 Building REAL250005052643 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052643' /scratch/stefan/7921156/working/building/REAL250005052643 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052643 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052643/0 /scratch/stefan/7921156/working/building/REAL250005052643 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/794 `/scratch/stefan/7921156/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(Cl)=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052643.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052643 none CC(Cl)=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 98, 98, 98, 68, 31, 68, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 98, 68, 68, 68, 68, 31, 31, 11, 1] 137 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: 497 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052643 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052643 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052643/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052643 Building REAL250005052644 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052644' /scratch/stefan/7921156/working/building/REAL250005052644 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052644 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052644/0 /scratch/stefan/7921156/working/building/REAL250005052644 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/795 `/scratch/stefan/7921156/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052644.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052644 none CC=CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 96, 96, 96, 70, 30, 69, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 114, 96, 70, 70, 70, 70, 30, 30, 10, 1] 114 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: 439 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052644 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052644 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052644/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052644 Building REAL250005052645 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052645' /scratch/stefan/7921156/working/building/REAL250005052645 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052645 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052645/0 /scratch/stefan/7921156/working/building/REAL250005052645 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/796 `/scratch/stefan/7921156/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)(F)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052645.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052645 none CCC(F)(F)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 91, 184, 184, 91, 91, 52, 18, 51, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 91, 52, 52, 52, 52, 18, 18, 6, 1] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 961 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052645 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052645 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052645/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052645 Building REAL250005052646 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052646' /scratch/stefan/7921156/working/building/REAL250005052646 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052646 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052646/0 /scratch/stefan/7921156/working/building/REAL250005052646 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/797 `/scratch/stefan/7921156/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC1F) `REAL250005052646.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052646 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [67, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 68, 99, 99, 99, 167, 167, 167, 167, 68, 68, 68, 68, 27, 27, 9, 1, 99, 167, 167, 167, 167, 167, 167] 167 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: 562 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: REAL250005052646 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [31, 6, 31, 103, 160, 160, 160, 167, 167, 167, 167, 167, 6, 1, 6, 1, 1, 1, 1, 1, 31, 31, 31, 31, 103, 103, 160, 167, 6, 2, 2, 2, 1, 1, 1] 167 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 597 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052646 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052646 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052646/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052646 Building REAL250005052647 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052647' /scratch/stefan/7921156/working/building/REAL250005052647 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052647 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052647/0 /scratch/stefan/7921156/working/building/REAL250005052647 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/798 `/scratch/stefan/7921156/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC(=O)O1) `REAL250005052647.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052647 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC(=O)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [84, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 86, 128, 128, 128, 176, 176, 176, 176, 176, 176, 86, 86, 86, 86, 28, 28, 9, 1, 128, 176, 176, 176, 176] 176 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]) total number of confs: 637 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052647 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC(=O)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [39, 10, 39, 119, 166, 166, 166, 176, 176, 176, 176, 176, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 119, 119, 166, 176, 10, 1, 1, 1, 1] 176 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 639 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052647 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052647 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052647/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052647 Building REAL250005052648 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052648' /scratch/stefan/7921156/working/building/REAL250005052648 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052648 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052648/0 /scratch/stefan/7921156/working/building/REAL250005052648 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/799 `/scratch/stefan/7921156/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CCF) `REAL250005052648.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052648 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 15, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [62, 31, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 62, 91, 91, 91, 123, 123, 137, 62, 62, 62, 62, 31, 31, 10, 1, 91, 123, 123, 137, 137] 137 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: 555 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052648 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052648 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052648/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052648 Building REAL250005052649 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052649' /scratch/stefan/7921156/working/building/REAL250005052649 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052649 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052649/0 /scratch/stefan/7921156/working/building/REAL250005052649 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/800 `/scratch/stefan/7921156/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)CC1CC1) `REAL250005052649.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052649 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)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.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [33, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 33, 59, 59, 59, 120, 120, 158, 201, 201, 33, 33, 33, 33, 10, 10, 3, 1, 59, 120, 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]) total number of confs: 880 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052649 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)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.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [93, 53, 93, 160, 201, 201, 201, 201, 201, 201, 201, 201, 53, 12, 53, 3, 12, 1, 1, 1, 1, 93, 93, 93, 93, 160, 160, 201, 201, 53, 12, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 799 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052649 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052649 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052649/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052649 Building REAL250005052650 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052650' /scratch/stefan/7921156/working/building/REAL250005052650 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052650 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052650/0 /scratch/stefan/7921156/working/building/REAL250005052650 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/801 `/scratch/stefan/7921156/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1COC(=O)N1) `REAL250005052650.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052650 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1COC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [50, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 52, 70, 70, 70, 85, 85, 85, 85, 85, 85, 52, 52, 52, 52, 22, 22, 8, 1, 70, 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]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052650 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1COC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [24, 10, 24, 56, 81, 81, 81, 85, 85, 85, 85, 85, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 56, 56, 81, 85, 10, 1, 1, 1] 85 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 311 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052650 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052650 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052650/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052650 Building REAL250005052651 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052651' /scratch/stefan/7921156/working/building/REAL250005052651 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052651 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052651/0 /scratch/stefan/7921156/working/building/REAL250005052651 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/802 `/scratch/stefan/7921156/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCCC#N) `REAL250005052651.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052651 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCCC#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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 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: [36, 19, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 36, 46, 46, 46, 118, 141, 156, 198, 198, 36, 36, 36, 36, 19, 19, 7, 1, 46, 118, 118, 150, 150, 158, 158, 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: 977 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052651 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052651 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052651/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052651 Building REAL250005052652 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052652' /scratch/stefan/7921156/working/building/REAL250005052652 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052652 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052652/0 /scratch/stefan/7921156/working/building/REAL250005052652 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/803 `/scratch/stefan/7921156/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CO)CC1) `REAL250005052652.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052652 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [56, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 58, 102, 102, 102, 191, 201, 191, 191, 58, 58, 58, 58, 18, 18, 6, 1, 102, 201, 201, 603, 191, 191, 191, 191] 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: 1311 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052652 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [26, 7, 26, 86, 181, 182, 182, 191, 191, 191, 191, 191, 7, 1, 7, 1, 1, 9, 1, 1, 26, 26, 26, 26, 86, 86, 182, 191, 7, 9, 9, 27, 1, 1, 1, 1] 603 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 680 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052652 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052652 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052652/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052652 Building REAL250005052653 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052653' /scratch/stefan/7921156/working/building/REAL250005052653 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052653 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052653/0 /scratch/stefan/7921156/working/building/REAL250005052653 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/804 `/scratch/stefan/7921156/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NO1) `REAL250005052653.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052653 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [59, 22, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 61, 83, 83, 83, 89, 89, 89, 89, 61, 61, 61, 61, 22, 22, 8, 1, 83, 89, 89] 89 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]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052653 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [22, 8, 22, 57, 87, 87, 87, 89, 89, 89, 89, 89, 8, 1, 8, 1, 1, 1, 1, 1, 22, 22, 22, 22, 57, 57, 87, 89, 8, 1, 1] 89 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052653 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052653 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052653/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052653 Building REAL250005052654 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052654' /scratch/stefan/7921156/working/building/REAL250005052654 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005052654 as failed and skipping /scratch/stefan/7921156/working /scratch/stefan/7921156 `/scratch/stefan/7921156/working/building/REAL250005052654' -> `/scratch/stefan/7921156/failed/REAL250005052654' Building REAL250005052655 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052655' /scratch/stefan/7921156/working/building/REAL250005052655 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052655 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052655/0 /scratch/stefan/7921156/working/building/REAL250005052655 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/805 `/scratch/stefan/7921156/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(=O)N1) `REAL250005052655.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052655 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [82, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 85, 122, 122, 122, 156, 156, 156, 156, 156, 85, 85, 85, 85, 32, 32, 9, 1, 122, 156, 156, 156, 156, 156, 156] 156 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: 584 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052655 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [37, 11, 37, 100, 147, 147, 147, 156, 156, 156, 156, 156, 11, 1, 11, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 100, 100, 147, 156, 11, 1, 1, 1, 1, 1, 1] 156 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 565 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052655 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052655 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052655/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052655 Building REAL250005052656 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052656' /scratch/stefan/7921156/working/building/REAL250005052656 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052656 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052656/0 /scratch/stefan/7921156/working/building/REAL250005052656 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/806 `/scratch/stefan/7921156/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)O) `REAL250005052656.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052656 none 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', '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'] dock atom type numbers: [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, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [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] 1 hydrogens need rotated 372 conformations in input total number of sets (complete confs): 372 using faster count positions algorithm for large data unique positions, atoms: [81, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 82, 115, 115, 115, 124, 124, 124, 82, 82, 82, 82, 37, 37, 11, 1, 115, 124, 124, 124, 372] 372 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: 853 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052656 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052656 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052656/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052656 Building REAL250005052657 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052657' /scratch/stefan/7921156/working/building/REAL250005052657 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052657 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052657/0 /scratch/stefan/7921156/working/building/REAL250005052657 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/807 `/scratch/stefan/7921156/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=C(F)O1) `REAL250005052657.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052657 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=C(F)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 15, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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: [72, 35, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 73, 110, 110, 110, 115, 115, 115, 115, 115, 73, 73, 73, 73, 35, 35, 9, 1, 110, 115, 115] 115 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]) 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: REAL250005052657 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=C(F)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 15, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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: [21, 7, 21, 62, 108, 108, 108, 115, 115, 115, 115, 115, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 62, 62, 108, 115, 7, 1, 1] 115 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 399 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052657 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052657 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052657/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052657 Building REAL250005052658 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052658' /scratch/stefan/7921156/working/building/REAL250005052658 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052658 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052658/0 /scratch/stefan/7921156/working/building/REAL250005052658 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/808 `/scratch/stefan/7921156/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052658.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052658 none CON=CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 122, 122, 122, 85, 32, 83, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 122, 85, 85, 85, 85, 32, 32, 8, 1] 146 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 557 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052658 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052658 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052658/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052658 Building REAL250005052659 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052659' /scratch/stefan/7921156/working/building/REAL250005052659 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052659 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052659/0 /scratch/stefan/7921156/working/building/REAL250005052659 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/809 `/scratch/stefan/7921156/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052659.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052659 none C#CCC(C)(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 148, 73, 148, 148, 73, 73, 48, 16, 47, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 148, 148, 148, 148, 148, 148, 73, 48, 48, 48, 48, 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: 895 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052659 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052659 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052659/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052659 Building REAL250005052660 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052660' /scratch/stefan/7921156/working/building/REAL250005052660 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052660 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052660/0 /scratch/stefan/7921156/working/building/REAL250005052660 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/810 `/scratch/stefan/7921156/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(F)C1) `REAL250005052660.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052660 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 80, 120, 120, 120, 201, 201, 201, 201, 201, 80, 80, 80, 80, 28, 28, 9, 1, 120, 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]) total number of confs: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052660 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [47, 11, 47, 134, 193, 193, 193, 201, 201, 201, 201, 201, 11, 1, 11, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 134, 134, 193, 201, 11, 1, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 36, 37, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 734 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052660 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052660 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052660/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052660 Building REAL250005052661 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052661' /scratch/stefan/7921156/working/building/REAL250005052661 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052661 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052661/0 /scratch/stefan/7921156/working/building/REAL250005052661 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/811 `/scratch/stefan/7921156/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(OC)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052661.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052661 none CCC(C)(OC)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 184, 106, 184, 183, 190, 106, 106, 59, 18, 57, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 184, 184, 184, 190, 190, 190, 106, 59, 59, 59, 59, 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: 935 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052661 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052661 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052661/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052661 Building REAL250005052662 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052662' /scratch/stefan/7921156/working/building/REAL250005052662 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052662 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052662/0 /scratch/stefan/7921156/working/building/REAL250005052662 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/812 `/scratch/stefan/7921156/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052662.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052662 none CC(C)[C@H](O)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 180, 201, 123, 180, 180, 123, 123, 70, 25, 66, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 540, 123, 70, 70, 70, 70, 25, 25, 7, 1] 603 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052662 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052662 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052662/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052662 Building REAL250005052663 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052663' /scratch/stefan/7921156/working/building/REAL250005052663 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052663 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052663/0 /scratch/stefan/7921156/working/building/REAL250005052663 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/813 `/scratch/stefan/7921156/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005052663.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052663 none C#CC1(C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 117, 193, 193, 193, 201, 201, 201, 201, 201, 1, 1, 1, 7, 34, 34, 34, 34, 117, 117, 193, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 32, 18, 19, 20, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 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: REAL250005052663 none C#CC1(C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 110, 110, 110, 73, 26, 71, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 110, 73, 73, 73, 73, 26, 26, 8, 1, 201, 201, 201, 201] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 699 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052663 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052663 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052663/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052663 Building REAL250005052664 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052664' /scratch/stefan/7921156/working/building/REAL250005052664 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052664 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052664/0 /scratch/stefan/7921156/working/building/REAL250005052664 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/814 `/scratch/stefan/7921156/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCC(=O)O1) `REAL250005052664.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052664 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCC(=O)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [77, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 79, 126, 126, 126, 177, 177, 177, 177, 177, 177, 79, 79, 79, 79, 27, 27, 9, 1, 126, 177, 177, 177, 177] 177 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]) total number of confs: 644 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052664 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCC(=O)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [40, 11, 40, 119, 168, 168, 168, 177, 177, 177, 177, 177, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 119, 119, 168, 177, 11, 1, 1, 1, 1] 177 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 645 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052664 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052664 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052664/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052664 Building REAL250005052665 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052665' /scratch/stefan/7921156/working/building/REAL250005052665 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052665 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052665/0 /scratch/stefan/7921156/working/building/REAL250005052665 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/815 `/scratch/stefan/7921156/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC=CCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052665.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052665 none C=CC=CCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 157, 68, 68, 68, 52, 17, 52, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 157, 157, 68, 52, 52, 52, 52, 17, 17, 4, 1] 201 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 809 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052665 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052665 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052665/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052665 Building REAL250005052666 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052666' /scratch/stefan/7921156/working/building/REAL250005052666 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052666 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052666/0 /scratch/stefan/7921156/working/building/REAL250005052666 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/816 `/scratch/stefan/7921156/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005052666.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052666 none C#CC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 116, 196, 196, 196, 201, 201, 201, 201, 201, 1, 1, 1, 1, 7, 34, 34, 34, 34, 116, 116, 196, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 36, 33, 35, 32, 34, 18, 19, 20, 21, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 716 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052666 none C#CC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 74, 27, 72, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 100, 74, 74, 74, 74, 27, 27, 8, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 685 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052666 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052666 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052666/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052666 Building REAL250005052667 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052667' /scratch/stefan/7921156/working/building/REAL250005052667 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005052667 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052667/0 /scratch/stefan/7921156/working/building/REAL250005052667 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/817 `/scratch/stefan/7921156/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC[N@@H+]1C) `REAL250005052667.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052667 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC[N@@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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 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]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052667 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC[N@@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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 6, 6, 6, 6, 7, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 7, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2] 7 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052667 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052667/1 /scratch/stefan/7921156/working/building/REAL250005052667 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/818 `/scratch/stefan/7921156/working/3D/818' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC[N@H+]1C) `REAL250005052667.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052667/1/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: REAL250005052667 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC[N@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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [17, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 20, 20, 20, 22, 22, 22, 22, 22, 22, 22, 17, 17, 17, 17, 12, 12, 8, 1, 20, 22, 22, 22, 22, 22, 22, 22, 22, 22] 22 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: 85 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: REAL250005052667 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC[N@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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 16, 17, 17, 17, 22, 22, 22, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 16, 16, 17, 22, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2] 22 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052667 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `2' /scratch/stefan/7921156/working/building/REAL250005052667/2 /scratch/stefan/7921156/working/building/REAL250005052667 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 2 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/819 `/scratch/stefan/7921156/working/3D/819' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCCN1C) `REAL250005052667.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005052667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052667/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052667 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 7, 5, 5, 5, 10, 5, 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, 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 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [82, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 84, 116, 116, 116, 121, 121, 121, 121, 121, 121, 84, 84, 84, 84, 30, 30, 7, 1, 116, 121, 121, 121, 121, 121, 121, 121, 121, 121] 121 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]) total number of confs: 464 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: REAL250005052667 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 7, 5, 5, 5, 10, 5, 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, 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 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [22, 7, 22, 65, 116, 116, 116, 121, 121, 121, 121, 121, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 65, 65, 116, 121, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2] 121 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39]) total number of confs: 424 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052667 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052667 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052667/0.* 2: /scratch/stefan/7921156/working/building/REAL250005052667/2.* 1: /scratch/stefan/7921156/working/building/REAL250005052667/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052667 Building REAL250005052668 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052668' /scratch/stefan/7921156/working/building/REAL250005052668 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052668 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052668/0 /scratch/stefan/7921156/working/building/REAL250005052668 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/820 `/scratch/stefan/7921156/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC=CCO1) `REAL250005052668.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052668 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC=CCO1 NO_LONG_NAME dock atom types: ['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.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, 1, 11, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [84, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 85, 124, 124, 124, 156, 156, 156, 156, 156, 85, 85, 85, 85, 36, 36, 11, 1, 124, 156, 156, 156, 156, 156, 156, 156] 156 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: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052668 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC=CCO1 NO_LONG_NAME dock atom types: ['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.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, 1, 11, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [34, 11, 34, 94, 147, 147, 147, 156, 156, 156, 156, 156, 11, 1, 11, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 94, 94, 147, 156, 11, 1, 1, 1, 1, 1, 1, 1] 156 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 558 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052668 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052668 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052668/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052668 Building REAL250005052669 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052669' /scratch/stefan/7921156/working/building/REAL250005052669 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052669 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052669/0 /scratch/stefan/7921156/working/building/REAL250005052669 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/821 `/scratch/stefan/7921156/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(C)(C)C1) `REAL250005052669.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052669 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(C)(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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [56, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 57, 88, 88, 88, 88, 88, 88, 88, 88, 57, 57, 57, 57, 26, 26, 9, 1, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88] 88 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: 332 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: REAL250005052669 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(C)(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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 53, 84, 84, 84, 88, 88, 88, 88, 88, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 53, 53, 84, 88, 6, 1, 2, 2, 2, 2, 2, 2, 1, 1] 88 rigid atoms, others: [37, 38, 13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 328 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052669 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052669 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052669/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052669 Building REAL250005052670 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052670' /scratch/stefan/7921156/working/building/REAL250005052670 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052670 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052670/0 /scratch/stefan/7921156/working/building/REAL250005052670 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/822 `/scratch/stefan/7921156/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#C[C@H]1C[C@H]1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052670.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052670 none C#C[C@H]1C[C@H]1C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 35, 35, 112, 179, 179, 179, 191, 191, 191, 191, 191, 1, 1, 1, 8, 35, 35, 35, 35, 112, 112, 179, 191] 191 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 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: REAL250005052670 none C#C[C@H]1C[C@H]1C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 191, 191, 191, 143, 191, 143, 143, 94, 39, 92, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 191, 191, 191, 143, 94, 94, 94, 94, 38, 38, 12, 1] 191 rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 704 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052670 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052670 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052670/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052670 Building REAL250005052671 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052671' /scratch/stefan/7921156/working/building/REAL250005052671 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052671 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052671/0 /scratch/stefan/7921156/working/building/REAL250005052671 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/823 `/scratch/stefan/7921156/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(N=[N+]=[N-])CC1) `REAL250005052671.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052671 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(N=[N+]=[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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 8, 8, 5, 5, 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, 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] 0 hydrogens 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, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 48, 80, 80, 80, 163, 201, 201, 163, 163, 48, 48, 48, 48, 18, 18, 6, 1, 80, 163, 163, 163, 163] 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: 600 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052671 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(N=[N+]=[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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 8, 8, 5, 5, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 9, 26, 74, 154, 154, 154, 163, 163, 163, 163, 163, 9, 1, 9, 1, 1, 13, 13, 1, 1, 26, 26, 26, 26, 74, 74, 154, 163, 9, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 15, 16, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 549 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052671 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052671 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052671/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052671 Building REAL250005052672 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052672' /scratch/stefan/7921156/working/building/REAL250005052672 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052672 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052672/0 /scratch/stefan/7921156/working/building/REAL250005052672 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/824 `/scratch/stefan/7921156/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)OC) `REAL250005052672.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052672 none CCC(CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [170, 164, 119, 62, 62, 62, 35, 13, 35, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 164, 166, 170, 170, 170, 170, 170, 164, 119, 119, 62, 35, 35, 35, 35, 13, 13, 5, 1, 166, 166, 166] 170 rigid atoms, others: [37, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 766 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052672 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052672 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052672/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052672 Building REAL250005052673 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052673' /scratch/stefan/7921156/working/building/REAL250005052673 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052673 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052673/0 /scratch/stefan/7921156/working/building/REAL250005052673 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/825 `/scratch/stefan/7921156/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSC=N1) `REAL250005052673.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052673 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSC=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.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [68, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 68, 91, 91, 91, 92, 92, 92, 92, 68, 68, 68, 68, 33, 33, 9, 1, 91, 92, 92] 92 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]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052673 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSC=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.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [15, 4, 15, 47, 86, 86, 86, 92, 92, 92, 92, 92, 4, 1, 4, 1, 1, 1, 1, 1, 15, 15, 15, 15, 47, 47, 86, 92, 4, 1, 1] 92 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 311 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052673 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052673 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052673/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052673 Building REAL250005052674 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052674' /scratch/stefan/7921156/working/building/REAL250005052674 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052674 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052674/0 /scratch/stefan/7921156/working/building/REAL250005052674 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/826 `/scratch/stefan/7921156/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(CC)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052674.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052674 none CC=C(CC)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 74, 164, 201, 74, 74, 44, 13, 44, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 201, 201, 201, 201, 201, 74, 44, 44, 44, 44, 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: 765 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052674 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052674 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052674/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052674 Building REAL250005052675 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052675' /scratch/stefan/7921156/working/building/REAL250005052675 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052675 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052675/0 /scratch/stefan/7921156/working/building/REAL250005052675 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/827 `/scratch/stefan/7921156/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC12CC(C1)C2) `REAL250005052675.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052675 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC12CC(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [78, 38, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 78, 94, 94, 94, 177, 177, 177, 177, 177, 78, 78, 78, 78, 38, 38, 12, 1, 94, 177, 177, 177, 177, 177, 177, 177, 177, 177] 177 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: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052675 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC12CC(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [74, 33, 74, 137, 166, 166, 166, 177, 177, 177, 177, 177, 33, 6, 33, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 137, 137, 166, 177, 33, 6, 6, 1, 1, 1, 1, 1, 1, 1] 177 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 677 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052675 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052675 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052675/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052675 Building REAL250005052676 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052676' /scratch/stefan/7921156/working/building/REAL250005052676 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052676 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052676/0 /scratch/stefan/7921156/working/building/REAL250005052676 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/828 `/scratch/stefan/7921156/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)C(C)O) `REAL250005052676.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052676 none CCC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)C(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 234 conformations in input total number of sets (complete confs): 234 using faster count positions algorithm for large data unique positions, atoms: [72, 68, 40, 40, 40, 30, 14, 30, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 68, 75, 77, 72, 72, 72, 72, 72, 68, 40, 30, 30, 30, 30, 14, 14, 6, 1, 77, 77, 77, 77, 231] 234 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 601 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052676 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052676 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052676/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052676 Building REAL250005052677 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052677' /scratch/stefan/7921156/working/building/REAL250005052677 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052677 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052677/0 /scratch/stefan/7921156/working/building/REAL250005052677 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/829 `/scratch/stefan/7921156/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052677.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052677 none COC(F)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 111, 197, 111, 111, 70, 23, 67, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 197, 111, 70, 70, 70, 70, 23, 23, 7, 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: 843 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052677 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052677 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052677/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052677 Building REAL250005052678 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052678' /scratch/stefan/7921156/working/building/REAL250005052678 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052678 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052678/0 /scratch/stefan/7921156/working/building/REAL250005052678 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/830 `/scratch/stefan/7921156/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C#N)CCC1) `REAL250005052678.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052678 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C#N)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.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [56, 22, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 57, 81, 81, 81, 131, 131, 131, 131, 131, 57, 57, 57, 57, 22, 22, 8, 1, 81, 131, 131, 131, 131, 131, 131] 131 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: 470 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: REAL250005052678 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C#N)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.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 23, 78, 123, 123, 123, 131, 131, 131, 131, 131, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 78, 78, 123, 131, 7, 1, 1, 1, 1, 1, 1] 131 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 465 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052678 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052678 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052678/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052678 Building REAL250005052679 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052679' /scratch/stefan/7921156/working/building/REAL250005052679 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052679 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052679/0 /scratch/stefan/7921156/working/building/REAL250005052679 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/831 `/scratch/stefan/7921156/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=C1CCCC1) `REAL250005052679.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052679 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 79, 115, 115, 115, 201, 201, 201, 201, 201, 79, 79, 79, 79, 25, 25, 7, 1, 115, 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]) total number of confs: 709 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052679 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=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.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 9, 46, 134, 197, 197, 197, 201, 201, 201, 201, 201, 9, 1, 9, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 134, 134, 197, 201, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 746 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052679 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052679 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052679/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052679 Building REAL250005052680 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052680' /scratch/stefan/7921156/working/building/REAL250005052680 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052680 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052680/0 /scratch/stefan/7921156/working/building/REAL250005052680 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/832 `/scratch/stefan/7921156/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(C)(C)C#N) `REAL250005052680.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052680 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 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 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [60, 28, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 61, 91, 91, 91, 152, 186, 186, 186, 186, 61, 61, 61, 61, 28, 28, 11, 1, 91, 152, 152, 186, 186, 186, 186, 186, 186] 186 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: 826 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052680 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052680 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052680/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052680 Building REAL250005052681 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052681' /scratch/stefan/7921156/working/building/REAL250005052681 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052681 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052681/0 /scratch/stefan/7921156/working/building/REAL250005052681 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/833 `/scratch/stefan/7921156/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052681.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052681 none COCC(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 129, 110, 81, 110, 81, 81, 54, 23, 54, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 110, 330, 81, 54, 54, 54, 54, 23, 23, 6, 1] 387 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: 915 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052681 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052681 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052681/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052681 Building REAL250005052682 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052682' /scratch/stefan/7921156/working/building/REAL250005052682 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052682 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052682/0 /scratch/stefan/7921156/working/building/REAL250005052682 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/834 `/scratch/stefan/7921156/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC1(F)F) `REAL250005052682.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052682 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC1(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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 79, 121, 121, 121, 201, 201, 201, 201, 201, 79, 79, 79, 79, 28, 28, 9, 1, 121, 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]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052682 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC1(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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 13, 50, 137, 193, 193, 193, 201, 201, 201, 201, 201, 13, 1, 13, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 137, 137, 193, 201, 13, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 746 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052682 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052682 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052682/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052682 Building REAL250005052683 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052683' /scratch/stefan/7921156/working/building/REAL250005052683 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052683 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052683/0 /scratch/stefan/7921156/working/building/REAL250005052683 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/835 `/scratch/stefan/7921156/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1C#N) `REAL250005052683.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052683 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [73, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 74, 104, 104, 104, 181, 181, 181, 181, 181, 181, 74, 74, 74, 74, 28, 28, 8, 1, 104, 181, 181] 181 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]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052683 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [46, 12, 46, 122, 173, 173, 173, 181, 181, 181, 181, 181, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 122, 122, 173, 181, 12, 1, 1] 181 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 667 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052683 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052683 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052683/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052683 Building REAL250005052684 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052684' /scratch/stefan/7921156/working/building/REAL250005052684 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052684 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052684/0 /scratch/stefan/7921156/working/building/REAL250005052684 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/836 `/scratch/stefan/7921156/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052684.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052684 none C=C(C)CCCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 121, 34, 34, 34, 25, 14, 25, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 195, 192, 155, 155, 121, 121, 34, 25, 25, 25, 25, 14, 14, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1005 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052684 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052684 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052684/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052684 Building REAL250005052685 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052685' /scratch/stefan/7921156/working/building/REAL250005052685 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052685 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052685/0 /scratch/stefan/7921156/working/building/REAL250005052685 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/837 `/scratch/stefan/7921156/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1C[C@@H](O)C1) `REAL250005052685.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052685 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [70, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 111, 111, 111, 201, 201, 201, 201, 201, 201, 71, 71, 71, 71, 29, 29, 9, 1, 111, 201, 201, 603, 201, 201] 603 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: 1289 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: REAL250005052685 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [47, 12, 47, 130, 191, 191, 191, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 130, 130, 191, 201, 12, 1, 1, 3, 1, 1] 603 rigid atoms, others: [32, 34, 35, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 726 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052685 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052685 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052685/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052685 Building REAL250005052686 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052686' /scratch/stefan/7921156/working/building/REAL250005052686 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052686 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052686/0 /scratch/stefan/7921156/working/building/REAL250005052686 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/838 `/scratch/stefan/7921156/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC1(C)C) `REAL250005052686.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052686 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC1(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 67, 67, 67, 183, 201, 201, 201, 201, 45, 45, 45, 45, 16, 16, 4, 1, 67, 183, 183, 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: 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: REAL250005052686 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC1(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens 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, 40, 91, 165, 201, 201, 201, 201, 201, 201, 201, 201, 40, 5, 40, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 165, 165, 201, 201, 40, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 832 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052686 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052686 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052686/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052686 Building REAL250005052687 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052687' /scratch/stefan/7921156/working/building/REAL250005052687 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052687 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052687/0 /scratch/stefan/7921156/working/building/REAL250005052687 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/839 `/scratch/stefan/7921156/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=C(Cl)CC1) `REAL250005052687.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052687 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=C(Cl)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.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 16, 5, 5, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [68, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 108, 108, 108, 129, 129, 129, 129, 69, 69, 69, 69, 29, 29, 9, 1, 108, 129, 129, 129, 129] 129 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]) total number of confs: 445 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052687 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=C(Cl)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.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 16, 5, 5, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [33, 12, 33, 80, 122, 122, 122, 129, 129, 129, 129, 129, 12, 1, 12, 1, 1, 1, 1, 1, 33, 33, 33, 33, 80, 80, 122, 129, 12, 1, 1, 1, 1] 129 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 458 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052687 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052687 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052687/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052687 Building REAL250005052688 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052688' /scratch/stefan/7921156/working/building/REAL250005052688 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052688 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052688/0 /scratch/stefan/7921156/working/building/REAL250005052688 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/840 `/scratch/stefan/7921156/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](F)C2) `REAL250005052688.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052688 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](F)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'F', 'C.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, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 78, 100, 100, 100, 201, 201, 201, 201, 201, 201, 201, 78, 78, 78, 78, 32, 32, 9, 1, 100, 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]) total number of confs: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052688 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](F)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'F', 'C.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, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 7, 34, 118, 192, 192, 192, 201, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 118, 118, 192, 201, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 706 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052688 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052688 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052688/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052688 Building REAL250005052689 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052689' /scratch/stefan/7921156/working/building/REAL250005052689 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052689 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052689/0 /scratch/stefan/7921156/working/building/REAL250005052689 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/841 `/scratch/stefan/7921156/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNC(=O)O1) `REAL250005052689.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052689 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNC(=O)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 6, 3, 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: [64, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 64, 97, 97, 97, 102, 102, 102, 102, 102, 64, 64, 64, 64, 26, 26, 9, 1, 97, 102, 102] 102 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]) 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: REAL250005052689 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNC(=O)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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 6, 3, 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: [21, 8, 21, 60, 100, 100, 100, 102, 102, 102, 102, 102, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 60, 60, 100, 102, 8, 1, 1] 102 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 363 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052689 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052689 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052689/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052689 Building REAL250005052690 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052690' /scratch/stefan/7921156/working/building/REAL250005052690 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052690 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052690/0 /scratch/stefan/7921156/working/building/REAL250005052690 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/842 `/scratch/stefan/7921156/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1C[C@H]1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052690.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052690 none CC(C)[C@@H]1C[C@H]1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 130, 197, 197, 197, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 4, 4, 1, 1, 12, 50, 50, 50, 50, 130, 130, 197, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052690 none CC(C)[C@@H]1C[C@H]1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 102, 201, 102, 102, 73, 26, 70, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 73, 73, 73, 73, 25, 25, 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: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052690 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052690 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052690/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052690 Building REAL250005052691 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052691' /scratch/stefan/7921156/working/building/REAL250005052691 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052691 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052691/0 /scratch/stefan/7921156/working/building/REAL250005052691 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/843 `/scratch/stefan/7921156/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COCCO) `REAL250005052691.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052691 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COCCO NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [32, 10, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 32, 46, 46, 46, 95, 164, 199, 201, 32, 32, 32, 32, 10, 10, 4, 1, 46, 95, 95, 199, 199, 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: 1322 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052691 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052691 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052691/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052691 Building REAL250005052692 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052692' /scratch/stefan/7921156/working/building/REAL250005052692 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052692 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052692/0 /scratch/stefan/7921156/working/building/REAL250005052692 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/844 `/scratch/stefan/7921156/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)CF) `REAL250005052692.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052692 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(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', '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, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 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, 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: [58, 21, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 60, 110, 110, 110, 192, 192, 192, 201, 60, 60, 60, 60, 21, 21, 6, 1, 110, 192, 192, 192, 192, 192, 192, 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: 829 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052692 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052692 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052692/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052692 Building REAL250005052693 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052693' /scratch/stefan/7921156/working/building/REAL250005052693 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052693 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052693/0 /scratch/stefan/7921156/working/building/REAL250005052693 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/845 `/scratch/stefan/7921156/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052693.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052693 none CC(C)[C@@H](O)CC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 576 conformations in input total number of sets (complete confs): 576 using faster count positions algorithm for large data unique positions, atoms: [192, 146, 192, 121, 146, 146, 71, 71, 71, 39, 16, 39, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 192, 192, 192, 438, 121, 121, 71, 39, 39, 39, 39, 16, 16, 5, 1] 576 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: 1355 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052693 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052693 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052693/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052693 Building REAL250005052694 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052694' /scratch/stefan/7921156/working/building/REAL250005052694 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052694 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052694/0 /scratch/stefan/7921156/working/building/REAL250005052694 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/846 `/scratch/stefan/7921156/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)CO) `REAL250005052694.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052694 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [63, 22, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 65, 114, 114, 114, 190, 191, 190, 201, 65, 65, 65, 65, 22, 22, 6, 1, 114, 190, 191, 191, 191, 191, 191, 200, 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, 36, 37]) total number of confs: 1453 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052694 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052694 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052694/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052694 Building REAL250005052695 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052695' /scratch/stefan/7921156/working/building/REAL250005052695 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052695 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052695/0 /scratch/stefan/7921156/working/building/REAL250005052695 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/847 `/scratch/stefan/7921156/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052695.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052695 none C=CCC(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 146, 71, 146, 71, 71, 47, 18, 47, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 146, 146, 146, 146, 71, 47, 47, 47, 47, 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: 909 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052695 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052695 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052695/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052695 Building REAL250005052696 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052696' /scratch/stefan/7921156/working/building/REAL250005052696 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052696 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052696/0 /scratch/stefan/7921156/working/building/REAL250005052696 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/848 `/scratch/stefan/7921156/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCC1C) `REAL250005052696.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052696 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [47, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 49, 62, 62, 62, 65, 65, 65, 65, 65, 49, 49, 49, 49, 22, 22, 9, 1, 62, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65] 65 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: 252 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: REAL250005052696 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 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: [10, 3, 10, 33, 62, 62, 62, 65, 65, 65, 65, 65, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 33, 33, 62, 65, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 65 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40]) total number of confs: 237 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052696 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052696 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052696/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052696 Building REAL250005052697 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052697' /scratch/stefan/7921156/working/building/REAL250005052697 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052697 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052697/0 /scratch/stefan/7921156/working/building/REAL250005052697 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/849 `/scratch/stefan/7921156/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC[C@@H]2C[C@@H]21) `REAL250005052697.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052697 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 72, 109, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 72, 72, 72, 72, 25, 25, 9, 1, 109, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 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, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 697 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: REAL250005052697 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 12, 54, 147, 196, 196, 196, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 147, 147, 196, 201, 12, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 750 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052697 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052697 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052697/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052697 Building REAL250005052698 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052698' /scratch/stefan/7921156/working/building/REAL250005052698 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052698 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052698/0 /scratch/stefan/7921156/working/building/REAL250005052698 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/850 `/scratch/stefan/7921156/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(F)C1) `REAL250005052698.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052698 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [69, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 70, 94, 94, 94, 187, 187, 187, 187, 187, 70, 70, 70, 70, 27, 27, 10, 1, 94, 187, 187, 187, 187, 187, 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, 35, 36, 37]) total number of confs: 631 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: REAL250005052698 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [33, 7, 33, 115, 177, 177, 177, 187, 187, 187, 187, 187, 7, 1, 7, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 115, 115, 177, 187, 7, 2, 2, 2, 1, 1, 1, 1, 1] 187 rigid atoms, others: [33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 654 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052698 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052698 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052698/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052698 Building REAL250005052699 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052699' /scratch/stefan/7921156/working/building/REAL250005052699 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052699 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052699/0 /scratch/stefan/7921156/working/building/REAL250005052699 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/851 `/scratch/stefan/7921156/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1C) `REAL250005052699.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052699 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 29, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 80, 117, 117, 117, 201, 201, 201, 201, 201, 80, 80, 80, 80, 29, 29, 9, 1, 117, 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]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052699 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 12, 52, 135, 192, 192, 192, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 135, 135, 192, 201, 12, 1, 1, 2, 2, 2] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 742 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052699 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052699 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052699/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052699 Building REAL250005052700 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052700' /scratch/stefan/7921156/working/building/REAL250005052700 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052700 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052700/0 /scratch/stefan/7921156/working/building/REAL250005052700 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/852 `/scratch/stefan/7921156/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)O) `REAL250005052700.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052700 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 423 conformations in input total number of sets (complete confs): 423 using faster count positions algorithm for large data unique positions, atoms: [88, 39, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 88, 118, 118, 118, 141, 141, 141, 88, 88, 88, 88, 39, 39, 10, 1, 118, 141, 141, 141, 141, 141, 141, 423] 423 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: 995 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052700 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052700 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052700/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052700 Building REAL250005052701 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052701' /scratch/stefan/7921156/working/building/REAL250005052701 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052701 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052701/0 /scratch/stefan/7921156/working/building/REAL250005052701 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/853 `/scratch/stefan/7921156/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005052701.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052701 none CSC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 10, 10, 10, 39, 39, 110, 174, 174, 174, 181, 181, 181, 181, 181, 1, 1, 8, 8, 8, 10, 39, 39, 39, 39, 110, 110, 174, 181, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 35, 33, 34, 18, 19] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 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: REAL250005052701 none CSC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 109, 109, 109, 65, 20, 63, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 181, 181, 201, 201, 201, 109, 65, 65, 65, 65, 20, 20, 7, 1, 181, 181, 181, 181] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052701 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052701 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052701/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052701 Building REAL250005052702 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052702' /scratch/stefan/7921156/working/building/REAL250005052702 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052702 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052702/0 /scratch/stefan/7921156/working/building/REAL250005052702 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/854 `/scratch/stefan/7921156/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NOCC1) `REAL250005052702.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052702 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 12, 5, 5, 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, 3, 7, 3, 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 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [70, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 108, 108, 108, 117, 117, 117, 117, 71, 71, 71, 71, 30, 30, 9, 1, 108, 117, 117, 117, 117] 117 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]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052702 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 12, 5, 5, 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, 3, 7, 3, 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 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [32, 13, 32, 81, 115, 115, 115, 117, 117, 117, 117, 117, 13, 1, 13, 1, 1, 1, 1, 1, 32, 32, 32, 32, 81, 81, 115, 117, 13, 1, 1, 1, 1] 117 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 440 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052702 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052702 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052702/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052702 Building REAL250005052703 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052703' /scratch/stefan/7921156/working/building/REAL250005052703 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052703 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052703/0 /scratch/stefan/7921156/working/building/REAL250005052703 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/855 `/scratch/stefan/7921156/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052703.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052703 none CC(C#N)CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 90, 90, 90, 53, 20, 53, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 174, 174, 90, 53, 53, 53, 53, 20, 20, 6, 1] 201 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 866 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052703 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052703 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052703/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052703 Building REAL250005052704 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052704' /scratch/stefan/7921156/working/building/REAL250005052704 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005052704 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052704/0 /scratch/stefan/7921156/working/building/REAL250005052704 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/856 `/scratch/stefan/7921156/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@H+](C)C1CC1) `REAL250005052704.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052704 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@H+](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.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 16, 16, 16, 20, 21, 21, 21, 21, 21, 12, 12, 12, 12, 8, 8, 3, 1, 16, 20, 20, 21, 21, 21, 21, 21, 21, 21, 21] 21 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: 96 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: REAL250005052704 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@H+](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.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 20, 21, 21, 21, 21, 21, 21, 21, 21, 12, 7, 12, 2, 1, 2, 2, 1, 1, 1, 16, 16, 16, 16, 20, 20, 21, 21, 12, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1] 21 rigid atoms, others: [36, 37, 38, 39, 40, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052704 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052704/1 /scratch/stefan/7921156/working/building/REAL250005052704 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/857 `/scratch/stefan/7921156/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@@H+](C)C1CC1) `REAL250005052704.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052704/1/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: REAL250005052704 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@@H+](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.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 12, 12, 12, 14, 15, 15, 15, 15, 15, 10, 10, 10, 10, 9, 9, 4, 1, 12, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 15 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: 62 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: REAL250005052704 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@@H+](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.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 6, 9, 2, 1, 2, 2, 1, 1, 1, 12, 12, 12, 12, 15, 15, 15, 15, 9, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1] 15 rigid atoms, others: [36, 37, 38, 39, 40, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 71 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052704 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `2' /scratch/stefan/7921156/working/building/REAL250005052704/2 /scratch/stefan/7921156/working/building/REAL250005052704 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 2 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/858 `/scratch/stefan/7921156/working/3D/858' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(C)C1CC1) `REAL250005052704.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005052704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052704/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052704 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(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.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [43, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 66, 66, 66, 87, 88, 88, 88, 88, 45, 45, 45, 45, 16, 16, 4, 1, 66, 87, 87, 88, 88, 88, 88, 88, 88, 88, 88] 88 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: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052704 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(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.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [30, 14, 30, 59, 88, 88, 88, 88, 88, 88, 88, 88, 14, 8, 14, 3, 1, 3, 1, 1, 1, 30, 30, 30, 30, 59, 59, 88, 88, 14, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1] 88 rigid atoms, others: [35, 36, 37, 38, 39, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 346 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052704 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052704 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052704/0.* 2: /scratch/stefan/7921156/working/building/REAL250005052704/2.* 1: /scratch/stefan/7921156/working/building/REAL250005052704/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052704 Building REAL250005052705 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052705' /scratch/stefan/7921156/working/building/REAL250005052705 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052705 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052705/0 /scratch/stefan/7921156/working/building/REAL250005052705 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/859 `/scratch/stefan/7921156/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCOC1CC1) `REAL250005052705.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052705 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCOC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 5, 12, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 49, 49, 110, 123, 167, 201, 201, 35, 35, 35, 35, 14, 14, 4, 1, 49, 110, 110, 123, 123, 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: 729 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: REAL250005052705 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCOC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 5, 12, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 93, 127, 166, 201, 201, 201, 201, 201, 201, 201, 201, 93, 38, 93, 23, 6, 1, 1, 1, 1, 127, 127, 127, 127, 166, 166, 201, 201, 93, 38, 38, 23, 23, 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: 821 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052705 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052705 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052705/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052705 Building REAL250005052706 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052706' /scratch/stefan/7921156/working/building/REAL250005052706 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052706 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052706/0 /scratch/stefan/7921156/working/building/REAL250005052706 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/860 `/scratch/stefan/7921156/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCCCO) `REAL250005052706.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052706 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCCCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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, 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: [32, 14, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 32, 38, 38, 38, 108, 134, 162, 178, 199, 32, 32, 32, 32, 14, 14, 5, 1, 38, 108, 108, 155, 155, 161, 162, 201, 201, 198, 191, 597] 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: 1754 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052706 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052706 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052706/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052706 Building REAL250005052707 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052707' /scratch/stefan/7921156/working/building/REAL250005052707 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052707 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052707/0 /scratch/stefan/7921156/working/building/REAL250005052707 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/861 `/scratch/stefan/7921156/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)CCO) `REAL250005052707.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052707 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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', '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, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 438 conformations in input total number of sets (complete confs): 438 using faster count positions algorithm for large data unique positions, atoms: [31, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 126, 126, 146, 146, 31, 31, 31, 31, 12, 12, 4, 1, 50, 126, 126, 126, 126, 146, 146, 146, 146, 438] 438 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: 1071 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052707 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052707 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052707/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052707 Building REAL250005052708 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052708' /scratch/stefan/7921156/working/building/REAL250005052708 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052708 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052708/0 /scratch/stefan/7921156/working/building/REAL250005052708 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/862 `/scratch/stefan/7921156/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)=CC1CC1) `REAL250005052708.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052708 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)=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.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 15, 1, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 68, 123, 123, 123, 152, 153, 153, 201, 201, 68, 68, 68, 68, 21, 21, 4, 1, 123, 153, 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]) total number of confs: 733 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: REAL250005052708 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)=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.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 15, 1, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 38, 81, 152, 201, 201, 201, 201, 201, 201, 201, 201, 38, 8, 37, 8, 8, 1, 1, 1, 1, 81, 81, 81, 81, 152, 152, 201, 201, 38, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 767 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052708 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052708 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052708/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052708 Building REAL250005052709 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052709' /scratch/stefan/7921156/working/building/REAL250005052709 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052709 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052709/0 /scratch/stefan/7921156/working/building/REAL250005052709 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/863 `/scratch/stefan/7921156/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(F)C1) `REAL250005052709.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052709 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [47, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 47, 73, 73, 73, 170, 201, 201, 201, 201, 47, 47, 47, 47, 18, 18, 5, 1, 73, 170, 170, 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: 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: REAL250005052709 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [82, 35, 82, 159, 200, 200, 200, 201, 201, 201, 201, 201, 35, 6, 35, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 159, 159, 200, 201, 35, 6, 6, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 806 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052709 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052709 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052709/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052709 Building REAL250005052710 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052710' /scratch/stefan/7921156/working/building/REAL250005052710 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052710 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052710/0 /scratch/stefan/7921156/working/building/REAL250005052710 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/864 `/scratch/stefan/7921156/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](O)CF) `REAL250005052710.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052710 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 12, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7] dock color type numbers: [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] 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: [72, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 74, 122, 122, 122, 183, 183, 183, 201, 74, 74, 74, 74, 27, 27, 9, 1, 122, 549, 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]) total number of confs: 1388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052710 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052710 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052710/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052710 Building REAL250005052711 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052711' /scratch/stefan/7921156/working/building/REAL250005052711 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052711 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052711/0 /scratch/stefan/7921156/working/building/REAL250005052711 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/865 `/scratch/stefan/7921156/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CCO)CC1) `REAL250005052711.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052711 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CCO)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7] 1 hydrogens need rotated 384 conformations in input total number of sets (complete confs): 384 using faster count positions algorithm for large data unique positions, atoms: [34, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 34, 63, 63, 63, 104, 128, 128, 104, 104, 34, 34, 34, 34, 15, 15, 5, 1, 63, 128, 128, 128, 128, 384, 104, 104, 104, 104] 384 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: 887 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052711 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CCO)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7] 1 hydrogens need rotated 384 conformations in input total number of sets (complete confs): 384 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 20, 54, 98, 98, 98, 104, 104, 104, 104, 104, 7, 1, 7, 1, 1, 7, 12, 1, 1, 20, 20, 20, 20, 54, 54, 98, 104, 7, 7, 7, 12, 12, 36, 1, 1, 1, 1] 384 rigid atoms, others: [35, 36, 37, 38, 13, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 439 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052711 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052711 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052711/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052711 Building REAL250005052712 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052712' /scratch/stefan/7921156/working/building/REAL250005052712 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052712 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052712/0 /scratch/stefan/7921156/working/building/REAL250005052712 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/866 `/scratch/stefan/7921156/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052712.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052712 none CC(C)C(C)(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 201, 134, 196, 194, 134, 134, 78, 26, 76, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 196, 196, 196, 588, 134, 78, 78, 78, 78, 26, 26, 7, 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: 1455 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052712 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052712 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052712/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052712 Building REAL250005052713 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052713' /scratch/stefan/7921156/working/building/REAL250005052713 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052713 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052713/0 /scratch/stefan/7921156/working/building/REAL250005052713 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/867 `/scratch/stefan/7921156/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CCC1) `REAL250005052713.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052713 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 477 conformations in input total number of sets (complete confs): 477 using faster count positions algorithm for large data unique positions, atoms: [74, 30, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 75, 108, 108, 108, 159, 159, 159, 159, 75, 75, 75, 75, 30, 30, 10, 1, 108, 477, 159, 159, 159, 159, 159, 159] 477 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: 1048 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052713 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 477 conformations in input total number of sets (complete confs): 477 using faster count positions algorithm for large data unique positions, atoms: [39, 11, 39, 111, 153, 153, 153, 159, 159, 159, 159, 159, 11, 1, 11, 1, 1, 1, 1, 1, 39, 39, 39, 39, 111, 111, 153, 159, 11, 6, 1, 1, 1, 1, 1, 1] 477 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 579 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052713 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052713 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052713/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052713 Building REAL250005052714 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052714' /scratch/stefan/7921156/working/building/REAL250005052714 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052714 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052714/0 /scratch/stefan/7921156/working/building/REAL250005052714 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/868 `/scratch/stefan/7921156/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(O)C1CC1) `REAL250005052714.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052714 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [60, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 62, 108, 108, 108, 170, 170, 201, 201, 62, 62, 62, 62, 21, 21, 7, 1, 108, 170, 510, 201, 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: 1315 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: REAL250005052714 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [81, 35, 81, 154, 199, 199, 199, 201, 201, 201, 201, 201, 35, 8, 35, 1, 8, 1, 1, 1, 81, 81, 81, 81, 154, 154, 199, 201, 35, 8, 24, 1, 1, 1, 1, 1] 603 rigid atoms, others: [32, 33, 34, 35, 15, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 820 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052714 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052714 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052714/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052714 Building REAL250005052715 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052715' /scratch/stefan/7921156/working/building/REAL250005052715 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052715 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052715/0 /scratch/stefan/7921156/working/building/REAL250005052715 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/869 `/scratch/stefan/7921156/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NN=C1) `REAL250005052715.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052715 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NN=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 8, 1, 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, 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] 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: [42, 23, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 42, 66, 66, 66, 113, 116, 116, 116, 116, 42, 42, 42, 42, 23, 23, 10, 1, 66, 113, 113, 116, 116] 116 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: 487 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052715 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NN=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 8, 1, 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, 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] 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, 29, 58, 85, 103, 103, 103, 114, 114, 114, 114, 114, 29, 7, 29, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 85, 85, 103, 114, 29, 7, 7, 1, 1] 114 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052715 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052715 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052715/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052715 Building REAL250005052716 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052716' /scratch/stefan/7921156/working/building/REAL250005052716 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052716 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052716/0 /scratch/stefan/7921156/working/building/REAL250005052716 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/870 `/scratch/stefan/7921156/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052716.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052716 none C=C(C)CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 201, 112, 112, 112, 82, 32, 82, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 199, 199, 112, 82, 82, 82, 82, 32, 32, 9, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052716 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052716 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052716/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052716 Building REAL250005052717 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052717' /scratch/stefan/7921156/working/building/REAL250005052717 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052717 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052717/0 /scratch/stefan/7921156/working/building/REAL250005052717 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/871 `/scratch/stefan/7921156/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)C#N) `REAL250005052717.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052717 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 8, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [48, 19, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 50, 70, 70, 70, 100, 100, 100, 100, 50, 50, 50, 50, 19, 19, 8, 1, 70, 100, 100, 100, 100, 100, 100] 100 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: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052717 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052717 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052717/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052717 Building REAL250005052718 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052718' /scratch/stefan/7921156/working/building/REAL250005052718 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052718 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052718/0 /scratch/stefan/7921156/working/building/REAL250005052718 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/872 `/scratch/stefan/7921156/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052718.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052718 none CCSCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 160, 123, 70, 70, 70, 41, 15, 41, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 123, 123, 70, 41, 41, 41, 41, 15, 15, 4, 1] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 830 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052718 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052718 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052718/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052718 Building REAL250005052719 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052719' /scratch/stefan/7921156/working/building/REAL250005052719 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052719 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052719/0 /scratch/stefan/7921156/working/building/REAL250005052719 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/873 `/scratch/stefan/7921156/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)OCCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052719.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052719 none CC(=O)OCCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 5, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 154, 139, 59, 59, 59, 45, 18, 45, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 154, 154, 139, 139, 59, 45, 45, 45, 45, 18, 18, 4, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052719 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052719 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052719/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052719 Building REAL250005052720 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052720' /scratch/stefan/7921156/working/building/REAL250005052720 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052720 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052720/0 /scratch/stefan/7921156/working/building/REAL250005052720 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/874 `/scratch/stefan/7921156/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052720.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052720 none CC(C)=C(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 125, 156, 125, 125, 83, 33, 83, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 156, 156, 156, 156, 125, 83, 83, 83, 83, 33, 33, 9, 1] 156 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052720 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052720 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052720/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052720 Building REAL250005052721 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052721' /scratch/stefan/7921156/working/building/REAL250005052721 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052721 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052721/0 /scratch/stefan/7921156/working/building/REAL250005052721 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/875 `/scratch/stefan/7921156/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC1(C)N=N1) `REAL250005052721.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052721 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC1(C)N=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 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, 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: [29, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 29, 44, 44, 44, 138, 155, 201, 201, 201, 29, 29, 29, 29, 13, 13, 4, 1, 44, 138, 138, 164, 164, 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: 847 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052721 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC1(C)N=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 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, 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: [96, 56, 96, 165, 201, 201, 201, 201, 201, 201, 201, 201, 56, 12, 56, 8, 1, 1, 1, 1, 1, 96, 96, 96, 96, 165, 165, 201, 201, 56, 12, 12, 8, 8, 2, 2, 2] 201 rigid atoms, others: [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: 827 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052721 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052721 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052721/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052721 Building REAL250005052722 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052722' /scratch/stefan/7921156/working/building/REAL250005052722 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052722 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052722/0 /scratch/stefan/7921156/working/building/REAL250005052722 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/876 `/scratch/stefan/7921156/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052722.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052722 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)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', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [24, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 31, 31, 31, 31, 31, 31, 31, 31, 24, 24, 24, 24, 18, 18, 7, 1, 31, 31] 31 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052722 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)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', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [9, 3, 9, 18, 25, 25, 25, 31, 31, 31, 31, 31, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 18, 18, 25, 31, 3, 1] 31 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052722 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052722 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052722/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052722 Building REAL250005052723 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052723' /scratch/stefan/7921156/working/building/REAL250005052723 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052723 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052723/0 /scratch/stefan/7921156/working/building/REAL250005052723 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/877 `/scratch/stefan/7921156/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COC1COC1) `REAL250005052723.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052723 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COC1COC1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 57, 57, 57, 130, 170, 201, 201, 201, 35, 35, 35, 35, 12, 12, 4, 1, 57, 130, 130, 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: 732 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052723 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COC1COC1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 67, 106, 160, 201, 201, 201, 201, 201, 201, 201, 201, 67, 25, 67, 6, 1, 1, 1, 1, 1, 106, 106, 106, 106, 160, 160, 201, 201, 67, 25, 25, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 803 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052723 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052723 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052723/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052723 Building REAL250005052724 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052724' /scratch/stefan/7921156/working/building/REAL250005052724 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052724 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052724/0 /scratch/stefan/7921156/working/building/REAL250005052724 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/878 `/scratch/stefan/7921156/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@]12C[C@@H]1[C@H](C)C2) `REAL250005052724.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052724 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@]12C[C@@H]1[C@H](C)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [68, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 70, 92, 92, 92, 192, 192, 192, 192, 192, 192, 192, 70, 70, 70, 70, 27, 27, 9, 1, 92, 192, 192, 192, 192, 192, 192, 192] 192 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: 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: REAL250005052724 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@]12C[C@@H]1[C@H](C)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [33, 6, 33, 109, 182, 182, 182, 192, 192, 192, 192, 192, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 109, 109, 182, 192, 6, 1, 1, 2, 2, 2, 1, 1] 192 rigid atoms, others: [32, 33, 37, 38, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 674 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052724 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052724 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052724/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052724 Building REAL250005052725 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052725' /scratch/stefan/7921156/working/building/REAL250005052725 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052725 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052725/0 /scratch/stefan/7921156/working/building/REAL250005052725 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/879 `/scratch/stefan/7921156/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052725.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052725 none CNC(=O)CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 72, 81, 54, 54, 54, 39, 19, 39, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 72, 72, 54, 39, 39, 39, 39, 19, 19, 8, 1] 81 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052725 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052725 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052725/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052725 Building REAL250005052726 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052726' /scratch/stefan/7921156/working/building/REAL250005052726 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052726 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052726/0 /scratch/stefan/7921156/working/building/REAL250005052726 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/880 `/scratch/stefan/7921156/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN=CN1C) `REAL250005052726.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052726 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN=CN1C NO_LONG_NAME dock atom types: ['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.2', 'N.2', 'C.2', 'N.pl3', 'C.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, 1, 11, 1, 8, 8, 1, 8, 5, 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, 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] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [68, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 96, 96, 96, 96, 96, 96, 96, 96, 69, 69, 69, 69, 27, 27, 9, 1, 96, 96, 96, 96, 96] 96 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: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052726 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN=CN1C NO_LONG_NAME dock atom types: ['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.2', 'N.2', 'C.2', 'N.pl3', 'C.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, 1, 11, 1, 8, 8, 1, 8, 5, 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, 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] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [15, 4, 15, 53, 95, 95, 95, 96, 96, 96, 96, 96, 4, 1, 4, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 53, 53, 95, 96, 4, 1, 2, 2, 2] 96 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 346 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052726 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052726 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052726/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052726 Building REAL250005052727 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052727' /scratch/stefan/7921156/working/building/REAL250005052727 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052727 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052727/0 /scratch/stefan/7921156/working/building/REAL250005052727 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/881 `/scratch/stefan/7921156/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCO[C@H]1C) `REAL250005052727.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052727 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCO[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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 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: [67, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 104, 104, 104, 121, 121, 121, 121, 121, 121, 121, 69, 69, 69, 69, 25, 25, 9, 1, 104, 121, 121, 121, 121, 121, 121, 121] 121 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: 463 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: REAL250005052727 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCO[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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 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: [20, 5, 20, 72, 114, 114, 114, 121, 121, 121, 121, 121, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 72, 72, 114, 121, 5, 1, 1, 1, 1, 2, 2, 2] 121 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 438 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052727 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052727 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052727/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052727 Building REAL250005052728 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052728' /scratch/stefan/7921156/working/building/REAL250005052728 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052728 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052728/0 /scratch/stefan/7921156/working/building/REAL250005052728 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/882 `/scratch/stefan/7921156/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(F)C1) `REAL250005052728.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052728 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 15, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 30, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 72, 110, 110, 110, 201, 201, 201, 201, 72, 72, 72, 72, 30, 30, 10, 1, 110, 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]) total number of confs: 703 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052728 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 15, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 11, 44, 127, 192, 192, 192, 201, 201, 201, 201, 201, 11, 1, 11, 1, 1, 1, 1, 1, 44, 44, 44, 44, 127, 127, 192, 201, 11, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 711 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052728 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052728 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052728/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052728 Building REAL250005052729 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052729' /scratch/stefan/7921156/working/building/REAL250005052729 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052729 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052729/0 /scratch/stefan/7921156/working/building/REAL250005052729 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/883 `/scratch/stefan/7921156/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)C(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052729.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052729 none CCC(O)C(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 357 conformations in input total number of sets (complete confs): 357 using faster count positions algorithm for large data unique positions, atoms: [119, 113, 95, 113, 70, 95, 70, 70, 38, 16, 38, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 113, 339, 95, 95, 95, 95, 70, 38, 38, 38, 38, 16, 16, 5, 1] 357 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 859 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052729 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052729 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052729/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052729 Building REAL250005052730 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052730' /scratch/stefan/7921156/working/building/REAL250005052730 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052730 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052730/0 /scratch/stefan/7921156/working/building/REAL250005052730 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/884 `/scratch/stefan/7921156/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(=O)N1) `REAL250005052730.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052730 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 53, 87, 87, 87, 177, 201, 201, 201, 201, 53, 53, 53, 53, 20, 20, 6, 1, 87, 177, 177, 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: 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: REAL250005052730 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 43, 88, 163, 200, 200, 200, 201, 201, 201, 201, 201, 43, 7, 43, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 163, 163, 200, 201, 43, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 794 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052730 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052730 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052730/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052730 Building REAL250005052731 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052731' /scratch/stefan/7921156/working/building/REAL250005052731 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052731 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052731/0 /scratch/stefan/7921156/working/building/REAL250005052731 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/885 `/scratch/stefan/7921156/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(O)C1CCC1) `REAL250005052731.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052731 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 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, 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: [69, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 71, 121, 121, 121, 172, 172, 201, 201, 201, 71, 71, 71, 71, 26, 26, 8, 1, 121, 172, 516, 201, 201, 201, 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: 1309 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052731 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 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, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [78, 36, 78, 152, 198, 198, 198, 201, 201, 201, 201, 201, 36, 7, 36, 1, 7, 1, 1, 1, 1, 78, 78, 78, 78, 152, 152, 198, 201, 36, 7, 21, 1, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 778 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052731 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052731 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052731/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052731 Building REAL250005052732 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052732' /scratch/stefan/7921156/working/building/REAL250005052732 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052732 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052732/0 /scratch/stefan/7921156/working/building/REAL250005052732 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/886 `/scratch/stefan/7921156/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1C[NH+](C)C1) `REAL250005052732.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052732 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1C[NH+](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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [14, 11, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 15, 15, 15, 18, 18, 18, 18, 18, 18, 14, 14, 14, 14, 11, 11, 7, 1, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 18 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: 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: REAL250005052732 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1C[NH+](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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 16, 16, 16, 16, 18, 18, 18, 18, 18, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 16, 16, 16, 18, 8, 5, 5, 1, 1, 1, 2, 2, 2, 1, 1] 18 rigid atoms, others: [33, 34, 35, 39, 40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052732 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052732 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052732/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052732 Building REAL250005052733 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052733' /scratch/stefan/7921156/working/building/REAL250005052733 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052733 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052733/0 /scratch/stefan/7921156/working/building/REAL250005052733 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/887 `/scratch/stefan/7921156/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(O)C1) `REAL250005052733.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052733 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [75, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 77, 124, 124, 124, 201, 201, 201, 201, 201, 77, 77, 77, 77, 30, 30, 9, 1, 124, 201, 201, 201, 201, 201, 201, 603, 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: 1302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052733 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [43, 11, 43, 129, 192, 192, 192, 201, 201, 201, 201, 201, 11, 1, 11, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 129, 129, 192, 201, 11, 1, 1, 1, 2, 2, 2, 6, 1, 1] 603 rigid atoms, others: [32, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 738 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052733 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052733 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052733/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052733 Building REAL250005052734 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052734' /scratch/stefan/7921156/working/building/REAL250005052734 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052734 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052734/0 /scratch/stefan/7921156/working/building/REAL250005052734 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/888 `/scratch/stefan/7921156/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052734.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052734 none C=CCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 122, 122, 122, 89, 36, 89, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 200, 122, 89, 89, 89, 89, 36, 36, 10, 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: 876 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052734 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052734 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052734/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052734 Building REAL250005052735 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052735' /scratch/stefan/7921156/working/building/REAL250005052735 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052735 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052735/0 /scratch/stefan/7921156/working/building/REAL250005052735 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/889 `/scratch/stefan/7921156/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[NH+](C)C) `REAL250005052735.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052735 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 14, 14, 14, 14, 13, 13, 13, 13, 9, 9, 6, 1, 14, 14, 14, 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052735 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052735/1 /scratch/stefan/7921156/working/building/REAL250005052735 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/890 `/scratch/stefan/7921156/working/3D/890' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(C)C) `REAL250005052735.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052735/1/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: REAL250005052735 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [95, 41, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 97, 141, 141, 141, 192, 192, 192, 97, 97, 97, 97, 41, 41, 10, 1, 141, 192, 192, 192, 192, 192, 192, 192, 192] 192 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: 814 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052735 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052735 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052735/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052735/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052735 Building REAL250005052736 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052736' /scratch/stefan/7921156/working/building/REAL250005052736 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052736 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052736/0 /scratch/stefan/7921156/working/building/REAL250005052736 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/891 `/scratch/stefan/7921156/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC#N) `REAL250005052736.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052736 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [55, 26, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 55, 76, 76, 76, 108, 108, 55, 55, 55, 55, 26, 26, 10, 1, 76, 108, 108] 108 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]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052736 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052736 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052736/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052736 Building REAL250005052737 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052737' /scratch/stefan/7921156/working/building/REAL250005052737 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052737 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052737/0 /scratch/stefan/7921156/working/building/REAL250005052737 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/892 `/scratch/stefan/7921156/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1F) `REAL250005052737.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052737 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 15, 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, 3, 7, 3, 4, 7, 6, 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: [82, 35, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 83, 117, 117, 117, 186, 186, 186, 83, 83, 83, 83, 35, 35, 10, 1, 117, 186, 186, 186, 186] 186 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: 669 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052737 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 15, 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, 3, 7, 3, 4, 7, 6, 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: [49, 12, 49, 119, 180, 180, 180, 186, 186, 186, 186, 186, 12, 1, 12, 1, 1, 1, 1, 49, 49, 49, 49, 119, 119, 180, 186, 12, 1, 1, 1, 1] 186 rigid atoms, others: [13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 674 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052737 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052737 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052737/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052737 Building REAL250005052738 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052738' /scratch/stefan/7921156/working/building/REAL250005052738 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052738 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052738/0 /scratch/stefan/7921156/working/building/REAL250005052738 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/893 `/scratch/stefan/7921156/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)[NH+](C)C) `REAL250005052738.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052738 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 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, 7, 7, 3, 7, 3, 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] 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: [14, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 16, 16, 16, 17, 17, 17, 14, 14, 14, 14, 13, 13, 8, 1, 14, 16, 16, 16, 17, 17, 17, 17, 17, 17] 17 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]) total number of confs: 68 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052738 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052738/1 /scratch/stefan/7921156/working/building/REAL250005052738 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/894 `/scratch/stefan/7921156/working/3D/894' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)N(C)C) `REAL250005052738.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052738/1/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: REAL250005052738 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 10, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [70, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 72, 96, 96, 96, 121, 121, 121, 123, 123, 72, 72, 72, 72, 31, 31, 10, 1, 96, 121, 121, 121, 123, 123, 123, 123, 123, 123] 123 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: 503 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052738 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052738 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052738/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052738/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052738 Building REAL250005052739 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052739' /scratch/stefan/7921156/working/building/REAL250005052739 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052739 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052739/0 /scratch/stefan/7921156/working/building/REAL250005052739 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/895 `/scratch/stefan/7921156/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCF) `REAL250005052739.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052739 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 15, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 25, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 70, 106, 106, 106, 198, 201, 70, 70, 70, 70, 25, 25, 8, 1, 106, 198, 198, 201, 201] 201 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]) total number of confs: 802 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052739 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052739 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052739/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052739 Building REAL250005052740 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052740' /scratch/stefan/7921156/working/building/REAL250005052740 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052740 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052740/0 /scratch/stefan/7921156/working/building/REAL250005052740 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/896 `/scratch/stefan/7921156/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(F)=NN1) `REAL250005052740.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052740 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(F)=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'H', 'H', 'H', '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, 1, 11, 1, 1, 1, 15, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [47, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 47, 74, 74, 74, 82, 82, 82, 82, 82, 47, 47, 47, 47, 21, 21, 9, 1, 74, 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]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052740 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(F)=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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'H', 'H', 'H', '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, 1, 11, 1, 1, 1, 15, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 17, 46, 76, 76, 76, 82, 82, 82, 82, 82, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 46, 46, 76, 82, 7, 1, 1] 82 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052740 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052740 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052740/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052740 Building REAL250005052741 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052741' /scratch/stefan/7921156/working/building/REAL250005052741 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052741 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052741/0 /scratch/stefan/7921156/working/building/REAL250005052741 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/897 `/scratch/stefan/7921156/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1C=CCC1) `REAL250005052741.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052741 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [72, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 74, 115, 115, 115, 201, 201, 201, 201, 74, 74, 74, 74, 31, 31, 10, 1, 115, 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]) total number of confs: 692 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: REAL250005052741 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [42, 11, 42, 134, 193, 193, 193, 201, 201, 201, 201, 201, 11, 1, 11, 1, 1, 1, 1, 1, 42, 42, 42, 42, 134, 134, 193, 201, 11, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 738 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052741 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052741 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052741/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052741 Building REAL250005052742 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052742' /scratch/stefan/7921156/working/building/REAL250005052742 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052742 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052742/0 /scratch/stefan/7921156/working/building/REAL250005052742 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/898 `/scratch/stefan/7921156/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)COC1) `REAL250005052742.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052742 none CCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)COC1 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', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 7, 7, 7, 26, 26, 91, 151, 151, 151, 157, 157, 157, 157, 157, 1, 1, 1, 3, 3, 3, 3, 3, 7, 26, 26, 26, 26, 91, 91, 151, 157, 1, 1, 1, 1] 157 rigid atoms, others: [1, 2, 3, 36, 37, 35, 18, 19, 20, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 569 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052742 none CCC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)COC1 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', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 87, 87, 87, 57, 23, 55, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 157, 157, 157, 157, 87, 57, 57, 57, 57, 23, 23, 8, 1, 157, 157, 157, 157] 157 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: 533 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052742 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052742 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052742/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052742 Building REAL250005052743 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052743' /scratch/stefan/7921156/working/building/REAL250005052743 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052743 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052743/0 /scratch/stefan/7921156/working/building/REAL250005052743 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/899 `/scratch/stefan/7921156/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC(C)(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052743.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052743 none C#CC(C)(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 111, 189, 189, 111, 111, 82, 35, 80, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 189, 189, 189, 189, 189, 189, 189, 111, 82, 82, 82, 82, 35, 35, 9, 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: 787 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052743 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052743 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052743/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052743 Building REAL250005052744 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052744' /scratch/stefan/7921156/working/building/REAL250005052744 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052744 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052744/0 /scratch/stefan/7921156/working/building/REAL250005052744 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/900 `/scratch/stefan/7921156/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CNC(=O)N1) `REAL250005052744.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052744 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CNC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [58, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 60, 87, 87, 87, 100, 100, 100, 100, 100, 100, 60, 60, 60, 60, 21, 21, 7, 1, 87, 100, 100, 100, 100] 100 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]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052744 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CNC(=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.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [23, 10, 23, 72, 94, 94, 94, 100, 100, 100, 100, 100, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 72, 72, 94, 100, 10, 1, 1, 1, 1] 100 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 366 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052744 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052744 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052744/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052744 Building REAL250005052745 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052745' /scratch/stefan/7921156/working/building/REAL250005052745 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005052745 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052745/0 /scratch/stefan/7921156/working/building/REAL250005052745 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/901 `/scratch/stefan/7921156/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1CCC1C) `REAL250005052745.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052745 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', '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, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 78, 139, 139, 139, 198, 201, 201, 201, 201, 78, 78, 78, 78, 25, 25, 8, 1, 139, 198, 198, 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]) total number of confs: 809 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: REAL250005052745 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', '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, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 23, 64, 153, 198, 198, 198, 201, 201, 201, 201, 201, 23, 5, 23, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 153, 153, 198, 201, 23, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 776 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052745 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052745/1 /scratch/stefan/7921156/working/building/REAL250005052745 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/902 `/scratch/stefan/7921156/working/3D/902' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@@H+]1CCC1C) `REAL250005052745.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052745/1/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: REAL250005052745 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@@H+]1CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', '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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 4, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 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: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052745 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@@H+]1CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', '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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 6, 6, 6, 6, 8, 8, 8, 8, 8, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 8, 4, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2] 8 rigid atoms, others: [33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052745 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `2' /scratch/stefan/7921156/working/building/REAL250005052745/2 /scratch/stefan/7921156/working/building/REAL250005052745 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 2 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/903 `/scratch/stefan/7921156/working/3D/903' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@H+]1CCC1C) `REAL250005052745.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005052745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052745/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052745 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@H+]1CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', '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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 20, 20, 20, 26, 26, 26, 26, 26, 26, 15, 15, 15, 15, 13, 13, 8, 1, 20, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 26 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: 99 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: REAL250005052745 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@H+]1CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', '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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 18, 19, 19, 19, 19, 26, 26, 26, 26, 26, 13, 5, 13, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 19, 19, 19, 26, 13, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2] 26 rigid atoms, others: [33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 92 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052745 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052745 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052745/0.* 2: /scratch/stefan/7921156/working/building/REAL250005052745/2.* 1: /scratch/stefan/7921156/working/building/REAL250005052745/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052745 Building REAL250005052746 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052746' /scratch/stefan/7921156/working/building/REAL250005052746 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052746 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052746/0 /scratch/stefan/7921156/working/building/REAL250005052746 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/904 `/scratch/stefan/7921156/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CC[NH+](C)C) `REAL250005052746.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052746 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CC[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.2', 'O.2', 'C.2', 'C.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, 1, 11, 1, 1, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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, 14, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 16, 23, 23, 23, 29, 29, 29, 29, 29, 29, 16, 16, 16, 16, 14, 14, 10, 1, 23, 29, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052746 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052746 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052746/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052746 Building REAL250005052747 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052747' /scratch/stefan/7921156/working/building/REAL250005052747 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052747 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052747/0 /scratch/stefan/7921156/working/building/REAL250005052747 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/905 `/scratch/stefan/7921156/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCSC1) `REAL250005052747.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052747 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.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, 1, 11, 1, 1, 5, 14, 5, 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, 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] 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: [72, 29, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 74, 111, 111, 111, 154, 154, 154, 154, 74, 74, 74, 74, 29, 29, 12, 1, 111, 154, 154, 154, 154, 154] 154 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: 489 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: REAL250005052747 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.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, 1, 11, 1, 1, 5, 14, 5, 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, 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] 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: [38, 13, 38, 101, 143, 143, 143, 154, 154, 154, 154, 154, 13, 1, 13, 1, 1, 1, 1, 1, 38, 38, 38, 38, 101, 101, 143, 154, 13, 1, 1, 1, 1, 1] 154 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 574 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052747 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052747 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052747/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052747 Building REAL250005052748 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052748' /scratch/stefan/7921156/working/building/REAL250005052748 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052748 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052748/0 /scratch/stefan/7921156/working/building/REAL250005052748 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/906 `/scratch/stefan/7921156/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052748.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052748 none CO[C@H](C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 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, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 163, 129, 163, 163, 129, 129, 83, 32, 80, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 165, 165, 165, 163, 163, 163, 129, 83, 83, 83, 83, 32, 32, 9, 1] 165 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 660 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052748 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052748 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052748/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052748 Building REAL250005052749 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052749' /scratch/stefan/7921156/working/building/REAL250005052749 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052749 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052749/0 /scratch/stefan/7921156/working/building/REAL250005052749 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/907 `/scratch/stefan/7921156/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)CCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052749.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052749 none CC(=O)CCC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 35, 39, 30, 14, 14, 14, 12, 9, 12, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 39, 39, 39, 35, 35, 30, 30, 14, 12, 12, 12, 12, 9, 9, 5, 1] 39 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052749 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052749 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052749/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052749 Building REAL250005052750 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052750' /scratch/stefan/7921156/working/building/REAL250005052750 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052750 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052750/0 /scratch/stefan/7921156/working/building/REAL250005052750 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/908 `/scratch/stefan/7921156/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCC1O) `REAL250005052750.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052750 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCC1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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, 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: [63, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 64, 87, 87, 87, 96, 96, 96, 96, 96, 64, 64, 64, 64, 26, 26, 8, 1, 87, 96, 96, 96, 96, 96, 96, 96, 96, 288] 288 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: 649 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: REAL250005052750 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCC1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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, 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: [18, 6, 18, 60, 93, 93, 93, 96, 96, 96, 96, 96, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 60, 60, 93, 96, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3] 288 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38]) total number of confs: 353 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052750 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052750 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052750/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052750 Building REAL250005052751 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052751' /scratch/stefan/7921156/working/building/REAL250005052751 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052751 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052751/0 /scratch/stefan/7921156/working/building/REAL250005052751 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/909 `/scratch/stefan/7921156/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H](C)O) `REAL250005052751.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052751 none 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', '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'] dock atom type numbers: [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, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [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] 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, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 75, 107, 107, 107, 112, 112, 112, 75, 75, 75, 75, 33, 33, 10, 1, 107, 112, 112, 112, 336] 336 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: 769 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052751 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052751 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052751/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052751 Building REAL250005052752 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052752' /scratch/stefan/7921156/working/building/REAL250005052752 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052752 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052752/0 /scratch/stefan/7921156/working/building/REAL250005052752 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/910 `/scratch/stefan/7921156/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052752.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052752 none CC[NH+](CC)CC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 16, 16, 16, 13, 7, 13, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 13, 13, 13, 13, 7, 7, 3, 1] 18 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: 80 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052752 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052752 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052752/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052752 Building REAL250005052753 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052753' /scratch/stefan/7921156/working/building/REAL250005052753 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052753 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052753/0 /scratch/stefan/7921156/working/building/REAL250005052753 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/911 `/scratch/stefan/7921156/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1CCC1) `REAL250005052753.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052753 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 83, 142, 142, 142, 195, 201, 201, 201, 83, 83, 83, 83, 29, 29, 9, 1, 142, 195, 195, 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]) total number of confs: 824 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052753 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 27, 69, 140, 196, 196, 196, 201, 201, 201, 201, 201, 27, 6, 27, 1, 1, 1, 1, 1, 69, 69, 69, 69, 140, 140, 196, 201, 27, 6, 6, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 773 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052753 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052753/1 /scratch/stefan/7921156/working/building/REAL250005052753 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/912 `/scratch/stefan/7921156/working/3D/912' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[NH+]1CCC1) `REAL250005052753.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052753/1/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: REAL250005052753 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 5, 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: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052753 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 5, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 5, 3, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 8, 5, 3, 3, 1, 1, 1, 1, 1, 1] 8 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 26 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052753 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052753 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052753/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052753/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052753 Building REAL250005052754 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052754' /scratch/stefan/7921156/working/building/REAL250005052754 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052754 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052754/0 /scratch/stefan/7921156/working/building/REAL250005052754 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/913 `/scratch/stefan/7921156/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(O)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052754.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052754 none CC(C)C(O)CC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 585 conformations in input total number of sets (complete confs): 585 using faster count positions algorithm for large data unique positions, atoms: [195, 161, 195, 119, 161, 71, 71, 71, 42, 17, 42, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 195, 195, 195, 195, 195, 195, 195, 161, 483, 119, 119, 71, 42, 42, 42, 42, 17, 17, 5, 1] 585 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1425 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052754 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052754 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052754/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052754 Building REAL250005052755 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052755' /scratch/stefan/7921156/working/building/REAL250005052755 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052755 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052755/0 /scratch/stefan/7921156/working/building/REAL250005052755 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/914 `/scratch/stefan/7921156/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=O)C1) `REAL250005052755.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052755 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.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, 1, 11, 5, 5, 12, 1, 11, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 5, 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: [68, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 70, 108, 108, 108, 180, 180, 180, 180, 180, 70, 70, 70, 70, 30, 30, 11, 1, 108, 180, 180, 180, 180, 180] 180 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: 635 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: REAL250005052755 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=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.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.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, 1, 11, 5, 5, 12, 1, 11, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 5, 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: [39, 10, 39, 112, 166, 166, 166, 180, 180, 180, 180, 180, 10, 1, 10, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 112, 112, 166, 180, 10, 1, 1, 1, 1, 1] 180 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 647 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052755 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052755 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052755/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052755 Building REAL250005052756 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052756' /scratch/stefan/7921156/working/building/REAL250005052756 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052756 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052756/0 /scratch/stefan/7921156/working/building/REAL250005052756 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/915 `/scratch/stefan/7921156/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052756.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052756 none CC(O)C(C)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 109, 191, 109, 109, 66, 25, 64, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 191, 191, 191, 191, 109, 66, 66, 66, 66, 25, 25, 9, 1] 603 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1443 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052756 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052756 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052756/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052756 Building REAL250005052757 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052757' /scratch/stefan/7921156/working/building/REAL250005052757 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052757 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052757/0 /scratch/stefan/7921156/working/building/REAL250005052757 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/916 `/scratch/stefan/7921156/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CCOC1) `REAL250005052757.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052757 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CCOC1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 4, 7, 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: [72, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 74, 115, 115, 115, 156, 156, 156, 156, 156, 74, 74, 74, 74, 28, 28, 10, 1, 115, 468, 156, 156, 156, 156, 156, 156] 468 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: 1029 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: REAL250005052757 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CCOC1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 4, 7, 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: [37, 8, 37, 103, 152, 152, 152, 156, 156, 156, 156, 156, 8, 1, 8, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 103, 103, 152, 156, 8, 6, 1, 1, 1, 1, 1, 1] 468 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 583 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052757 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052757 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052757/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052757 Building REAL250005052758 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052758' /scratch/stefan/7921156/working/building/REAL250005052758 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052758 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052758/0 /scratch/stefan/7921156/working/building/REAL250005052758 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/917 `/scratch/stefan/7921156/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C#N)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052758.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052758 none CCC(C)(C#N)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [111, 109, 69, 109, 109, 109, 69, 69, 42, 19, 42, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 109, 109, 109, 69, 42, 42, 42, 42, 19, 19, 7, 1] 115 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: 513 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052758 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052758 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052758/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052758 Building REAL250005052759 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052759' /scratch/stefan/7921156/working/building/REAL250005052759 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052759 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052759/0 /scratch/stefan/7921156/working/building/REAL250005052759 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/918 `/scratch/stefan/7921156/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052759.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052759 none C=C1CC1C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 52, 52, 137, 195, 195, 195, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 13, 52, 52, 52, 52, 137, 137, 195, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 747 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: REAL250005052759 none C=C1CC1C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 72, 29, 71, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 112, 72, 72, 72, 72, 29, 29, 9, 1] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 663 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052759 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052759 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052759/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052759 Building REAL250005052760 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052760' /scratch/stefan/7921156/working/building/REAL250005052760 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052760 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052760/0 /scratch/stefan/7921156/working/building/REAL250005052760 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/919 `/scratch/stefan/7921156/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC=CC1) `REAL250005052760.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052760 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 1, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 47, 70, 70, 70, 183, 201, 201, 201, 201, 47, 47, 47, 47, 18, 18, 4, 1, 70, 183, 183, 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: 814 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052760 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 1, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 38, 91, 157, 201, 201, 201, 201, 201, 201, 201, 201, 38, 6, 38, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 157, 157, 201, 201, 38, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 810 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052760 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052760 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052760/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052760 Building REAL250005052761 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052761' /scratch/stefan/7921156/working/building/REAL250005052761 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052761 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052761/0 /scratch/stefan/7921156/working/building/REAL250005052761 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/920 `/scratch/stefan/7921156/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)NC(=O)CC1OCCO1) `REAL250005052761.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052761 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1OCCO1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 58, 90, 90, 90, 169, 201, 201, 201, 201, 58, 58, 58, 58, 22, 22, 7, 1, 90, 169, 169, 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: 812 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052761 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1OCCO1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 45, 94, 166, 200, 200, 200, 201, 201, 201, 201, 201, 45, 10, 45, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 166, 166, 200, 201, 45, 10, 10, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 806 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052761 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052761 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052761/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052761 Building REAL250005052762 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052762' /scratch/stefan/7921156/working/building/REAL250005052762 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052762 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052762/0 /scratch/stefan/7921156/working/building/REAL250005052762 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/921 `/scratch/stefan/7921156/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(OC)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052762.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052762 none COC(OC)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 161, 83, 161, 193, 83, 83, 45, 15, 43, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 198, 198, 198, 161, 193, 193, 193, 83, 45, 45, 45, 45, 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: 801 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052762 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052762 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052762/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052762 Building REAL250005052763 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052763' /scratch/stefan/7921156/working/building/REAL250005052763 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052763 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052763/0 /scratch/stefan/7921156/working/building/REAL250005052763 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/922 `/scratch/stefan/7921156/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)NC(=O)CC1(C#N)CC1) `REAL250005052763.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052763 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(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', 'N.am', 'C.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 5, 1, 8, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 61, 97, 97, 97, 183, 201, 201, 201, 201, 61, 61, 61, 61, 24, 24, 9, 1, 97, 183, 183, 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: 823 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052763 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(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', 'N.am', 'C.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 5, 1, 8, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 29, 69, 138, 183, 183, 183, 201, 201, 201, 201, 201, 29, 6, 29, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 138, 138, 183, 201, 29, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 743 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052763 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052763 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052763/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052763 Building REAL250005052764 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052764' /scratch/stefan/7921156/working/building/REAL250005052764 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052764 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052764/0 /scratch/stefan/7921156/working/building/REAL250005052764 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/923 `/scratch/stefan/7921156/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052764.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052764 none COC(=O)CCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 150, 201, 127, 56, 56, 56, 36, 16, 36, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 150, 150, 127, 127, 56, 36, 36, 36, 36, 16, 16, 4, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 835 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052764 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052764 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052764/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052764 Building REAL250005052765 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052765' /scratch/stefan/7921156/working/building/REAL250005052765 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052765 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052765/0 /scratch/stefan/7921156/working/building/REAL250005052765 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/924 `/scratch/stefan/7921156/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCOC1) `REAL250005052765.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052765 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', '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, 1, 11, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [70, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 106, 106, 106, 183, 183, 183, 183, 183, 71, 71, 71, 71, 28, 28, 9, 1, 106, 183, 183, 183, 183, 183, 183, 183] 183 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: 520 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052765 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', '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, 1, 11, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [45, 12, 45, 112, 172, 172, 172, 183, 183, 183, 183, 183, 11, 1, 11, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 112, 112, 172, 183, 12, 1, 1, 1, 1, 1, 1, 1] 183 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 676 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052765 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052765 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052765/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052765 Building REAL250005052766 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052766' /scratch/stefan/7921156/working/building/REAL250005052766 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052766 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052766/0 /scratch/stefan/7921156/working/building/REAL250005052766 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/925 `/scratch/stefan/7921156/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(O)C(C)(C)C) `REAL250005052766.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052766 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 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, 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: [70, 31, 11, 12, 1, 12, 1, 1, 1, 1, 1, 1, 71, 87, 87, 87, 95, 95, 95, 95, 95, 71, 71, 71, 71, 31, 31, 12, 1, 87, 95, 285, 95, 95, 95, 95, 95, 95, 95, 95, 95] 285 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: 663 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052766 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052766 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052766/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052766 Building REAL250005052767 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052767' /scratch/stefan/7921156/working/building/REAL250005052767 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052767 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052767/0 /scratch/stefan/7921156/working/building/REAL250005052767 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/926 `/scratch/stefan/7921156/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)COC1) `REAL250005052767.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052767 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [56, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 57, 69, 69, 69, 153, 153, 153, 153, 57, 57, 57, 57, 21, 21, 9, 1, 69, 153, 153, 153, 153, 153, 153, 153] 153 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: 497 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: REAL250005052767 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [31, 6, 31, 96, 145, 145, 145, 153, 153, 153, 153, 153, 6, 1, 6, 1, 1, 1, 1, 1, 31, 31, 31, 31, 96, 96, 145, 153, 6, 2, 2, 2, 1, 1, 1, 1] 153 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 553 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052767 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052767 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052767/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052767 Building REAL250005052768 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052768' /scratch/stefan/7921156/working/building/REAL250005052768 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052768 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052768/0 /scratch/stefan/7921156/working/building/REAL250005052768 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/927 `/scratch/stefan/7921156/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCCO1) `REAL250005052768.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052768 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', '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, 1, 11, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [61, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 61, 85, 85, 85, 93, 93, 93, 93, 93, 61, 61, 61, 61, 28, 28, 9, 1, 85, 93, 93, 93, 93, 93, 93, 93] 93 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: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052768 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', '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, 1, 11, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [21, 7, 21, 54, 85, 85, 85, 93, 93, 93, 93, 93, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 54, 54, 85, 93, 7, 1, 1, 1, 1, 1, 1, 1] 93 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052768 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052768 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052768/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052768 Building REAL250005052769 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052769' /scratch/stefan/7921156/working/building/REAL250005052769 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052769 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052769/0 /scratch/stefan/7921156/working/building/REAL250005052769 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/928 `/scratch/stefan/7921156/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CCCO1) `REAL250005052769.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052769 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 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, 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: [86, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 88, 132, 132, 132, 161, 161, 161, 161, 161, 88, 88, 88, 88, 35, 35, 11, 1, 132, 161, 161, 161, 161, 161, 161, 161, 161, 161] 161 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: 606 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052769 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 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, 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: [33, 8, 33, 95, 150, 150, 150, 161, 161, 161, 161, 161, 8, 1, 8, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 95, 95, 150, 161, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1] 161 rigid atoms, others: [33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 573 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052769 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052769 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052769/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052769 Building REAL250005052770 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052770' /scratch/stefan/7921156/working/building/REAL250005052770 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052770 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052770/0 /scratch/stefan/7921156/working/building/REAL250005052770 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/929 `/scratch/stefan/7921156/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(=O)N1) `REAL250005052770.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052770 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [53, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 55, 86, 86, 86, 118, 118, 118, 118, 55, 55, 55, 55, 23, 23, 9, 1, 86, 118, 118, 118, 118] 118 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]) total number of confs: 424 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: REAL250005052770 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [37, 12, 37, 82, 113, 113, 113, 118, 118, 118, 118, 118, 12, 1, 12, 1, 1, 1, 1, 1, 37, 37, 37, 37, 82, 82, 113, 118, 12, 1, 1, 1, 1] 118 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 440 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052770 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052770 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052770/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052770 Building REAL250005052771 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052771' /scratch/stefan/7921156/working/building/REAL250005052771 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052771 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052771/0 /scratch/stefan/7921156/working/building/REAL250005052771 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/930 `/scratch/stefan/7921156/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC(=O)N1) `REAL250005052771.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052771 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 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: [56, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 58, 91, 91, 91, 121, 121, 121, 121, 121, 58, 58, 58, 58, 22, 22, 10, 1, 91, 121, 121, 121] 121 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]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052771 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 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: [31, 11, 31, 80, 114, 114, 114, 121, 121, 121, 121, 121, 11, 1, 11, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 80, 80, 114, 121, 11, 1, 1, 1] 121 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052771 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052771 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052771/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052771 Building REAL250005052772 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052772' /scratch/stefan/7921156/working/building/REAL250005052772 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052772 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052772/0 /scratch/stefan/7921156/working/building/REAL250005052772 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/931 `/scratch/stefan/7921156/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCCC1) `REAL250005052772.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052772 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 1, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [74, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 76, 99, 99, 99, 161, 161, 161, 161, 161, 76, 76, 76, 76, 29, 29, 9, 1, 99, 161, 161, 161, 161, 161, 161, 161, 161, 161] 161 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: 496 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052772 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 1, 5, 5, 5, 5, 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, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [44, 11, 44, 107, 150, 150, 150, 161, 161, 161, 161, 161, 11, 1, 11, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 107, 107, 150, 161, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 161 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 592 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052772 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052772 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052772/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052772 Building REAL250005052773 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052773' /scratch/stefan/7921156/working/building/REAL250005052773 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052773 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052773/0 /scratch/stefan/7921156/working/building/REAL250005052773 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/932 `/scratch/stefan/7921156/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052773.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052773 none CCC[C@H](O)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 149, 92, 149, 149, 92, 92, 57, 20, 55, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 199, 192, 192, 447, 92, 57, 57, 57, 57, 20, 20, 4, 1] 603 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1391 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052773 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052773 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052773/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052773 Building REAL250005052774 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052774' /scratch/stefan/7921156/working/building/REAL250005052774 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052774 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052774/0 /scratch/stefan/7921156/working/building/REAL250005052774 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/933 `/scratch/stefan/7921156/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(C)C1) `REAL250005052774.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052774 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 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: [73, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 73, 97, 97, 97, 199, 199, 199, 199, 199, 73, 73, 73, 73, 33, 33, 10, 1, 97, 199, 199, 199, 199, 199, 199, 199, 199, 199, 199, 199] 199 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: 667 number of broken/clashed sets: 199 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052774 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 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: [33, 6, 33, 112, 184, 184, 184, 199, 199, 199, 199, 199, 6, 1, 6, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 112, 112, 184, 199, 6, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1] 199 rigid atoms, others: [33, 34, 35, 39, 40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 702 number of broken/clashed sets: 199 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052774 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052774 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052774/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052774 Building REAL250005052775 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052775' /scratch/stefan/7921156/working/building/REAL250005052775 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052775 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052775/0 /scratch/stefan/7921156/working/building/REAL250005052775 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/934 `/scratch/stefan/7921156/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)N1CCC1) `REAL250005052775.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052775 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)N1CCC1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [79, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 81, 132, 132, 132, 149, 149, 149, 149, 149, 81, 81, 81, 81, 33, 33, 10, 1, 132, 149, 149, 149, 149, 149, 149, 149, 149, 149, 149] 149 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: 574 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: REAL250005052775 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)N1CCC1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [39, 12, 39, 102, 141, 141, 141, 149, 149, 149, 149, 149, 12, 3, 12, 1, 3, 1, 1, 1, 1, 39, 39, 39, 39, 102, 102, 141, 149, 12, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1] 149 rigid atoms, others: [34, 35, 36, 37, 38, 39, 15, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 547 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052775 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052775/1 /scratch/stefan/7921156/working/building/REAL250005052775 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/935 `/scratch/stefan/7921156/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)[NH+]1CCC1) `REAL250005052775.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052775/1/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: REAL250005052775 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(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.2', 'O.2', 'C.3', '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, 1, 11, 5, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 6, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 9 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: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052775 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(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.2', 'O.2', 'C.3', '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, 1, 11, 5, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 7, 8, 8, 8, 9, 9, 9, 9, 9, 4, 3, 4, 1, 3, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 8, 9, 4, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [35, 36, 37, 38, 39, 40, 15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052775 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052775 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052775/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052775/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052775 Building REAL250005052776 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052776' /scratch/stefan/7921156/working/building/REAL250005052776 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052776 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052776/0 /scratch/stefan/7921156/working/building/REAL250005052776 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/936 `/scratch/stefan/7921156/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CC1(F)F) `REAL250005052776.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052776 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CC1(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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [73, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 75, 112, 112, 112, 190, 190, 190, 190, 190, 75, 75, 75, 75, 27, 27, 10, 1, 112, 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]) total number of confs: 656 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052776 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CC1(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.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [47, 13, 47, 136, 184, 184, 184, 190, 190, 190, 190, 190, 13, 1, 13, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 136, 136, 184, 190, 13, 1, 1] 190 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 702 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052776 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052776 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052776/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052776 Building REAL250005052777 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052777' /scratch/stefan/7921156/working/building/REAL250005052777 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052777 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052777/0 /scratch/stefan/7921156/working/building/REAL250005052777 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/937 `/scratch/stefan/7921156/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CNN=C1) `REAL250005052777.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052777 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', '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, 1, 11, 5, 1, 1, 8, 8, 1, 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, 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] 0 hydrogens 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, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 63, 118, 118, 118, 196, 201, 201, 201, 201, 63, 63, 63, 63, 27, 27, 9, 1, 118, 196, 196, 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: 830 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052777 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=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.2', 'O.2', 'C.3', '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, 1, 11, 5, 1, 1, 8, 8, 1, 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, 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] 0 hydrogens 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, 129, 193, 193, 193, 201, 201, 201, 201, 201, 22, 8, 22, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 129, 129, 193, 201, 22, 8, 8, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 778 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052777 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052777 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052777/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052777 Building REAL250005052778 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052778' /scratch/stefan/7921156/working/building/REAL250005052778 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052778 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052778/0 /scratch/stefan/7921156/working/building/REAL250005052778 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/938 `/scratch/stefan/7921156/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(=O)C1) `REAL250005052778.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052778 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(=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.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [71, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 72, 96, 96, 96, 178, 178, 178, 178, 178, 72, 72, 72, 72, 28, 28, 10, 1, 96, 178, 178, 178, 178, 178, 178, 178] 178 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: 608 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: REAL250005052778 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(=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.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [30, 7, 30, 106, 162, 162, 162, 178, 178, 178, 178, 178, 7, 1, 7, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 106, 106, 162, 178, 7, 2, 2, 2, 1, 1, 1, 1] 178 rigid atoms, others: [33, 34, 35, 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]) total number of confs: 621 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052778 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052778 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052778/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052778 Building REAL250005052779 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052779' /scratch/stefan/7921156/working/building/REAL250005052779 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052779 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052779/0 /scratch/stefan/7921156/working/building/REAL250005052779 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/939 `/scratch/stefan/7921156/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CNC=C1) `REAL250005052779.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052779 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CNC=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.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 38, 72, 72, 72, 126, 201, 201, 201, 201, 38, 38, 38, 38, 15, 15, 5, 1, 72, 126, 126, 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: 665 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: REAL250005052779 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CNC=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.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 19, 63, 131, 200, 200, 200, 201, 201, 201, 201, 201, 19, 7, 19, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 131, 131, 200, 201, 19, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 802 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052779 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052779 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052779/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052779 Building REAL250005052780 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052780' /scratch/stefan/7921156/working/building/REAL250005052780 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052780 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052780/0 /scratch/stefan/7921156/working/building/REAL250005052780 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/940 `/scratch/stefan/7921156/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052780.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052780 none CCCC(C)(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 144, 108, 144, 144, 108, 108, 63, 24, 61, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 144, 144, 144, 432, 108, 63, 63, 63, 63, 24, 24, 6, 1] 603 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052780 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052780 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052780/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052780 Building REAL250005052781 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052781' /scratch/stefan/7921156/working/building/REAL250005052781 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052781 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052781/0 /scratch/stefan/7921156/working/building/REAL250005052781 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/941 `/scratch/stefan/7921156/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)(C)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052781.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052781 none CCOC(C)(C)C(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 122, 190, 190, 122, 122, 67, 20, 65, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 190, 190, 190, 190, 190, 190, 122, 67, 67, 67, 67, 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: 824 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052781 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052781 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052781/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052781 Building REAL250005052782 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052782' /scratch/stefan/7921156/working/building/REAL250005052782 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052782 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052782/0 /scratch/stefan/7921156/working/building/REAL250005052782 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/942 `/scratch/stefan/7921156/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(=O)C1) `REAL250005052782.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052782 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(=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.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 1, 1, 1, 56, 90, 90, 90, 167, 201, 201, 201, 201, 56, 56, 56, 56, 20, 20, 5, 1, 90, 167, 167, 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: 837 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052782 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(=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.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 38, 88, 163, 201, 201, 201, 201, 201, 201, 201, 201, 38, 6, 38, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 163, 163, 201, 201, 38, 6, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 802 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052782 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052782 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052782/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052782 Building REAL250005052783 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052783' /scratch/stefan/7921156/working/building/REAL250005052783 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052783 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052783/0 /scratch/stefan/7921156/working/building/REAL250005052783 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/943 `/scratch/stefan/7921156/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CSC1) `REAL250005052783.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052783 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CSC1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [59, 22, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 59, 98, 98, 98, 168, 201, 201, 201, 59, 59, 59, 59, 22, 22, 7, 1, 98, 168, 168, 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: 853 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052783 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CSC1 NO_LONG_NAME dock atom types: ['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', '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, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [95, 41, 95, 164, 198, 198, 198, 201, 201, 201, 201, 201, 41, 8, 41, 1, 1, 1, 1, 1, 95, 95, 95, 95, 164, 164, 198, 201, 41, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 790 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052783 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052783 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052783/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052783 Building REAL250005052784 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052784' /scratch/stefan/7921156/working/building/REAL250005052784 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052784 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052784/0 /scratch/stefan/7921156/working/building/REAL250005052784 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/944 `/scratch/stefan/7921156/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(F)CCC1) `REAL250005052784.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052784 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [69, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 71, 108, 108, 108, 151, 151, 151, 151, 71, 71, 71, 71, 32, 32, 10, 1, 108, 151, 151, 151, 151, 151, 151] 151 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: 549 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052784 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [36, 10, 36, 100, 146, 146, 146, 151, 151, 151, 151, 151, 10, 1, 10, 1, 1, 1, 1, 1, 36, 36, 36, 36, 100, 100, 146, 151, 10, 1, 1, 1, 1, 1, 1] 151 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 552 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052784 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052784 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052784/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052784 Building REAL250005052785 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052785' /scratch/stefan/7921156/working/building/REAL250005052785 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052785 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052785/0 /scratch/stefan/7921156/working/building/REAL250005052785 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/945 `/scratch/stefan/7921156/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CN1) `REAL250005052785.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052785 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [48, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 49, 65, 65, 65, 72, 72, 72, 72, 49, 49, 49, 49, 18, 18, 8, 1, 65, 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]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052785 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 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: [23, 8, 23, 50, 69, 69, 69, 72, 72, 72, 72, 72, 7, 1, 7, 1, 1, 1, 1, 1, 23, 23, 23, 23, 50, 50, 69, 72, 8, 1, 1, 1] 72 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052785 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052785 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052785/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052785 Building REAL250005052786 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052786' /scratch/stefan/7921156/working/building/REAL250005052786 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052786 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052786/0 /scratch/stefan/7921156/working/building/REAL250005052786 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/946 `/scratch/stefan/7921156/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005052786.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052786 none CC1=NOC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 63, 109, 109, 109, 113, 113, 113, 113, 113, 1, 2, 2, 2, 6, 20, 20, 20, 20, 63, 63, 109, 113] 113 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052786 none CC1=NOC(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 97, 97, 97, 62, 27, 62, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 97, 62, 62, 62, 62, 27, 27, 8, 1] 113 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: 393 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052786 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052786 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052786/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052786 Building REAL250005052787 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052787' /scratch/stefan/7921156/working/building/REAL250005052787 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052787 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052787/0 /scratch/stefan/7921156/working/building/REAL250005052787 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/947 `/scratch/stefan/7921156/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052787.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052787 none CCOC(=O)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 130, 130, 52, 130, 34, 34, 34, 22, 13, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 52, 52, 34, 22, 22, 22, 22, 13, 13, 4, 1] 133 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: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052787 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052787 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052787/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052787 Building REAL250005052788 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052788' /scratch/stefan/7921156/working/building/REAL250005052788 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052788 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052788/0 /scratch/stefan/7921156/working/building/REAL250005052788 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/948 `/scratch/stefan/7921156/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(=O)C1) `REAL250005052788.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052788 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 11, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [71, 29, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 72, 108, 108, 108, 167, 167, 167, 167, 72, 72, 72, 72, 29, 29, 11, 1, 108, 167, 167, 167, 167, 167] 167 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: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052788 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 11, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [43, 11, 43, 113, 157, 157, 157, 167, 167, 167, 167, 167, 11, 1, 11, 1, 1, 1, 1, 1, 43, 43, 43, 43, 113, 113, 157, 167, 11, 1, 1, 1, 1, 1] 167 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 614 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052788 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052788 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052788/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052788 Building REAL250005052789 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052789' /scratch/stefan/7921156/working/building/REAL250005052789 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052789 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052789/0 /scratch/stefan/7921156/working/building/REAL250005052789 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/949 `/scratch/stefan/7921156/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=CN=N1) `REAL250005052789.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052789 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=CN=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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, 1, 11, 5, 8, 1, 1, 8, 8, 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, 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] 0 hydrogens 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, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 55, 85, 85, 85, 173, 201, 201, 201, 201, 55, 55, 55, 55, 26, 26, 9, 1, 85, 173, 173, 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: 753 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052789 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=CN=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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, 1, 11, 5, 8, 1, 1, 8, 8, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 46, 89, 151, 190, 190, 190, 201, 201, 201, 201, 201, 46, 9, 46, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 151, 151, 190, 201, 46, 9, 9, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 792 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052789 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052789 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052789/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052789 Building REAL250005052790 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052790' /scratch/stefan/7921156/working/building/REAL250005052790 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052790 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052790/0 /scratch/stefan/7921156/working/building/REAL250005052790 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/950 `/scratch/stefan/7921156/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005052790.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052790 none C=CC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 7, 7, 7, 30, 30, 99, 187, 189, 187, 201, 201, 201, 201, 201, 1, 1, 1, 5, 5, 5, 7, 30, 30, 30, 30, 99, 99, 189, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 36, 37, 35, 33, 34, 18, 19, 20, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 692 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052790 none C=CC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 62, 20, 61, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 100, 62, 62, 62, 62, 20, 20, 4, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 682 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052790 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052790 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052790/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052790 Building REAL250005052791 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052791' /scratch/stefan/7921156/working/building/REAL250005052791 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052791 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052791/0 /scratch/stefan/7921156/working/building/REAL250005052791 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/951 `/scratch/stefan/7921156/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)COC1) `REAL250005052791.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052791 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 3, 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: [55, 24, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 57, 78, 78, 78, 111, 111, 111, 111, 57, 57, 57, 57, 24, 24, 10, 1, 78, 333, 111, 111, 111, 111] 333 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: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052791 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 3, 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: [32, 11, 32, 72, 104, 104, 104, 111, 111, 111, 111, 111, 11, 1, 11, 1, 1, 1, 1, 1, 32, 32, 32, 32, 72, 72, 104, 111, 11, 6, 1, 1, 1, 1] 333 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052791 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052791 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052791/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052791 Building REAL250005052792 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052792' /scratch/stefan/7921156/working/building/REAL250005052792 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052792 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052792/0 /scratch/stefan/7921156/working/building/REAL250005052792 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/952 `/scratch/stefan/7921156/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052792.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052792 none CCC(C)C(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 193, 165, 192, 112, 165, 112, 112, 70, 25, 68, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 193, 193, 165, 495, 112, 70, 70, 70, 70, 25, 25, 6, 1] 603 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1369 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052792 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052792 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052792/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052792 Building REAL250005052793 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052793' /scratch/stefan/7921156/working/building/REAL250005052793 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052793 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052793/0 /scratch/stefan/7921156/working/building/REAL250005052793 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/953 `/scratch/stefan/7921156/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1)=C1CC1) `REAL250005052793.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052793 none CC(C(=O)NC(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', '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'] dock atom type numbers: [5, 1, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [197, 123, 123, 123, 78, 33, 75, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 197, 123, 78, 78, 78, 78, 33, 33, 9, 1, 197, 197, 197, 197] 197 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: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052793 none CC(C(=O)NC(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', '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'] dock atom type numbers: [5, 1, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 12, 12, 12, 49, 49, 132, 187, 188, 187, 197, 197, 197, 197, 197, 1, 1, 1, 2, 2, 2, 12, 49, 49, 49, 49, 132, 132, 188, 197, 1, 1, 1, 1] 197 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 17, 18, 19] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 743 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052793 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052793 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052793/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052793 Building REAL250005052794 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052794' /scratch/stefan/7921156/working/building/REAL250005052794 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052794 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052794/0 /scratch/stefan/7921156/working/building/REAL250005052794 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/954 `/scratch/stefan/7921156/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052794.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052794 none CC1=CC1C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 61, 141, 196, 196, 196, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 13, 61, 61, 61, 61, 141, 141, 196, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 755 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052794 none CC1=CC1C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 114, 114, 114, 73, 26, 72, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 114, 73, 73, 73, 73, 26, 26, 8, 1] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 679 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052794 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052794 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052794/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052794 Building REAL250005052795 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052795' /scratch/stefan/7921156/working/building/REAL250005052795 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052795 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052795/0 /scratch/stefan/7921156/working/building/REAL250005052795 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/955 `/scratch/stefan/7921156/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(=O)N(C)C) `REAL250005052795.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052795 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 11, 8, 5, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [52, 20, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 54, 77, 77, 77, 91, 91, 91, 91, 54, 54, 54, 54, 20, 20, 6, 1, 77, 91, 91, 91, 91, 91, 91] 91 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: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052795 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052795 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052795/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052795 Building REAL250005052796 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052796' /scratch/stefan/7921156/working/building/REAL250005052796 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052796 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052796/0 /scratch/stefan/7921156/working/building/REAL250005052796 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/956 `/scratch/stefan/7921156/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005052796.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052796 none CC(=O)C1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 29, 29, 92, 167, 167, 167, 173, 173, 173, 173, 173, 1, 1, 5, 5, 5, 7, 29, 29, 29, 29, 92, 92, 167, 173, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 35, 33, 19, 20, 36] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 613 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052796 none CC(=O)C1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 88, 88, 88, 46, 15, 46, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 173, 173, 201, 201, 201, 88, 46, 46, 46, 46, 15, 15, 4, 1, 173, 173, 173, 173] 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: 687 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052796 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052796 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052796/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052796 Building REAL250005052797 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052797' /scratch/stefan/7921156/working/building/REAL250005052797 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052797 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052797/0 /scratch/stefan/7921156/working/building/REAL250005052797 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/957 `/scratch/stefan/7921156/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052797.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052797 none CCCC(O)C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 199, 135, 104, 135, 104, 104, 68, 24, 67, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 135, 405, 104, 68, 68, 68, 68, 24, 24, 5, 1] 603 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1323 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052797 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052797 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052797/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052797 Building REAL250005052798 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052798' /scratch/stefan/7921156/working/building/REAL250005052798 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052798 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052798/0 /scratch/stefan/7921156/working/building/REAL250005052798 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/958 `/scratch/stefan/7921156/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052798.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052798 none CCCCC(O)C(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [200, 183, 170, 114, 77, 114, 77, 77, 49, 15, 48, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 183, 182, 172, 172, 114, 342, 77, 49, 49, 49, 49, 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: 1319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052798 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052798 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052798/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052798 Building REAL250005052799 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052799' /scratch/stefan/7921156/working/building/REAL250005052799 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052799 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052799/0 /scratch/stefan/7921156/working/building/REAL250005052799 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/959 `/scratch/stefan/7921156/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CSC1CC1) `REAL250005052799.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052799 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CSC1CC1 NO_LONG_NAME dock atom types: ['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', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [29, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 29, 40, 40, 40, 109, 165, 201, 201, 29, 29, 29, 29, 13, 13, 4, 1, 40, 109, 109, 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: 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: REAL250005052799 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CSC1CC1 NO_LONG_NAME dock atom types: ['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', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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: [121, 84, 121, 175, 201, 201, 201, 201, 201, 201, 201, 201, 84, 27, 84, 6, 1, 1, 1, 1, 121, 121, 121, 121, 175, 175, 201, 201, 84, 27, 27, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 815 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052799 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052799 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052799/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052799 Building REAL250005052800 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052800' /scratch/stefan/7921156/working/building/REAL250005052800 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052800 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052800/0 /scratch/stefan/7921156/working/building/REAL250005052800 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/960 `/scratch/stefan/7921156/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)CC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052800.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052800 none CCC(O)CC(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 372 conformations in input total number of sets (complete confs): 372 using faster count positions algorithm for large data unique positions, atoms: [124, 122, 94, 122, 58, 58, 58, 35, 14, 35, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 122, 366, 94, 94, 58, 35, 35, 35, 35, 14, 14, 4, 1] 372 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: 920 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052800 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052800 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052800/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052800 Building REAL250005052801 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052801' /scratch/stefan/7921156/working/building/REAL250005052801 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052801 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052801/0 /scratch/stefan/7921156/working/building/REAL250005052801 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/961 `/scratch/stefan/7921156/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCC(=O)NC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005052801.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052801 none CNC(=O)CCC(=O)NC(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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 159, 198, 141, 80, 80, 80, 54, 26, 53, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 198, 198, 198, 198, 159, 159, 141, 141, 80, 54, 54, 54, 54, 26, 26, 10, 1] 198 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: 828 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052801 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052801 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052801/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052801 Building REAL250005052802 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052802' /scratch/stefan/7921156/working/building/REAL250005052802 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052802 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052802/0 /scratch/stefan/7921156/working/building/REAL250005052802 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/962 `/scratch/stefan/7921156/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCCF) `REAL250005052802.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052802 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 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, 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, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 34, 48, 48, 48, 146, 180, 200, 200, 34, 34, 34, 34, 13, 13, 4, 1, 48, 146, 146, 197, 197, 200, 200, 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: 985 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052802 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052802 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052802/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052802 Building REAL250005052803 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052803' /scratch/stefan/7921156/working/building/REAL250005052803 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052803 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052803/0 /scratch/stefan/7921156/working/building/REAL250005052803 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/963 `/scratch/stefan/7921156/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSN=C1) `REAL250005052803.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052803 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSN=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.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', '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, 1, 11, 1, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [60, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 61, 88, 88, 88, 115, 115, 115, 115, 61, 61, 61, 61, 21, 21, 9, 1, 88, 115, 115] 115 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]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052803 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSN=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.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', '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, 1, 11, 1, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [21, 5, 21, 75, 109, 109, 109, 115, 115, 115, 115, 115, 5, 1, 5, 1, 1, 1, 1, 1, 21, 21, 21, 21, 75, 75, 109, 115, 5, 1, 1] 115 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 416 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052803 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052803 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052803/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052803 Building REAL250005052804 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052804' /scratch/stefan/7921156/working/building/REAL250005052804 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052804 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052804/0 /scratch/stefan/7921156/working/building/REAL250005052804 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/964 `/scratch/stefan/7921156/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(=O)C1) `REAL250005052804.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052804 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(=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.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [67, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 116, 116, 116, 183, 183, 183, 183, 183, 69, 69, 69, 69, 27, 27, 9, 1, 116, 183, 183, 183, 183, 183, 183, 183] 183 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: 640 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: REAL250005052804 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(=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.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [41, 11, 41, 121, 174, 174, 174, 183, 183, 183, 183, 183, 11, 1, 11, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 121, 121, 174, 183, 11, 1, 1, 1, 1, 1, 1, 1] 183 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 663 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052804 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052804 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052804/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052804 Building REAL250005052805 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052805' /scratch/stefan/7921156/working/building/REAL250005052805 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052805 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052805/0 /scratch/stefan/7921156/working/building/REAL250005052805 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/965 `/scratch/stefan/7921156/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CC(=O)N1) `REAL250005052805.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052805 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 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: [50, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 52, 66, 66, 66, 90, 90, 90, 90, 90, 52, 52, 52, 52, 20, 20, 7, 1, 66, 90, 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]) total number of confs: 330 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: REAL250005052805 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 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: [30, 11, 30, 60, 87, 87, 87, 90, 90, 90, 90, 90, 11, 1, 11, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 60, 60, 87, 90, 11, 1, 1, 1] 90 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 338 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052805 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052805 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052805/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052805 Building REAL250005052806 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052806' /scratch/stefan/7921156/working/building/REAL250005052806 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052806 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052806/0 /scratch/stefan/7921156/working/building/REAL250005052806 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/966 `/scratch/stefan/7921156/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=N1) `REAL250005052806.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052806 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 1, 8, 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, 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] 0 hydrogens 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, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 59, 87, 87, 87, 165, 201, 201, 201, 201, 59, 59, 59, 59, 25, 25, 8, 1, 87, 165, 165, 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: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052806 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=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.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 1, 8, 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, 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] 0 hydrogens 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, 47, 88, 163, 196, 196, 196, 201, 201, 201, 201, 201, 47, 9, 47, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 163, 163, 196, 201, 47, 9, 9, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 798 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052806 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052806 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052806/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052806 Building REAL250005052807 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052807' /scratch/stefan/7921156/working/building/REAL250005052807 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052807 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052807/0 /scratch/stefan/7921156/working/building/REAL250005052807 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/967 `/scratch/stefan/7921156/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005052807.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052807 none COC1(C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 41, 41, 119, 178, 178, 178, 199, 199, 199, 199, 199, 1, 1, 4, 4, 4, 11, 41, 41, 41, 41, 119, 119, 178, 199, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 35, 33, 34, 18, 19] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 697 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052807 none COC1(C(=O)NC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 140, 140, 140, 89, 35, 87, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 199, 199, 201, 201, 201, 140, 89, 89, 89, 89, 35, 35, 10, 1, 199, 199, 199, 199] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 741 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052807 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052807 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052807/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052807 Building REAL250005052808 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052808' /scratch/stefan/7921156/working/building/REAL250005052808 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052808 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052808/0 /scratch/stefan/7921156/working/building/REAL250005052808 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/968 `/scratch/stefan/7921156/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CSC1) `REAL250005052808.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052808 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 14, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [75, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 76, 112, 112, 112, 162, 162, 162, 76, 76, 76, 76, 31, 31, 11, 1, 112, 162, 162, 162, 162, 162] 162 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]) total number of confs: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052808 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=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.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 14, 5, 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, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [38, 9, 38, 108, 149, 149, 149, 162, 162, 162, 162, 162, 9, 1, 9, 1, 1, 1, 1, 38, 38, 38, 38, 108, 108, 149, 162, 9, 1, 1, 1, 1, 1] 162 rigid atoms, others: [32, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 593 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052808 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052808 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052808/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052808 Building REAL250005052809 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052809' /scratch/stefan/7921156/working/building/REAL250005052809 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052809 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052809/0 /scratch/stefan/7921156/working/building/REAL250005052809 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/969 `/scratch/stefan/7921156/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=C(N)O1) `REAL250005052809.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052809 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=C(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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [51, 24, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 51, 81, 81, 81, 87, 87, 87, 87, 87, 51, 51, 51, 51, 24, 24, 8, 1, 81, 87, 87, 87] 87 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]) 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: REAL250005052809 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=C(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', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 50, 85, 85, 85, 87, 87, 87, 87, 87, 5, 1, 5, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 50, 50, 85, 87, 6, 1, 2, 2] 87 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 319 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052809 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052809 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052809/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052809 Building REAL250005052810 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052810' /scratch/stefan/7921156/working/building/REAL250005052810 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052810 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052810/0 /scratch/stefan/7921156/working/building/REAL250005052810 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/970 `/scratch/stefan/7921156/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(CO)CC1) `REAL250005052810.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052810 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7] 1 hydrogens need rotated 522 conformations in input total number of sets (complete confs): 522 using faster count positions algorithm for large data unique positions, atoms: [32, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 32, 42, 42, 42, 129, 163, 174, 163, 163, 32, 32, 32, 32, 14, 14, 4, 1, 42, 129, 129, 174, 174, 522, 163, 163, 163, 163] 522 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: 1232 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052810 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7] 1 hydrogens need rotated 522 conformations in input total number of sets (complete confs): 522 using faster count positions algorithm for large data unique positions, atoms: [64, 29, 64, 116, 162, 162, 162, 163, 163, 163, 163, 163, 29, 6, 29, 1, 1, 1, 8, 1, 1, 64, 64, 64, 64, 116, 116, 162, 163, 29, 6, 6, 8, 8, 24, 1, 1, 1, 1] 522 rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 699 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052810 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052810 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052810/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052810 Building REAL250005052811 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052811' /scratch/stefan/7921156/working/building/REAL250005052811 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052811 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052811/0 /scratch/stefan/7921156/working/building/REAL250005052811 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/971 `/scratch/stefan/7921156/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC=CO1) `REAL250005052811.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052811 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.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, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [87, 40, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 90, 135, 135, 135, 192, 192, 192, 192, 192, 90, 90, 90, 90, 40, 40, 11, 1, 135, 192, 192, 192, 192, 192, 192, 192] 192 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: 687 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: REAL250005052811 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC=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.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.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, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [40, 12, 40, 135, 185, 185, 185, 192, 192, 192, 192, 192, 12, 1, 12, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 135, 135, 185, 192, 12, 1, 1, 1, 1, 1, 1, 1] 192 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 703 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052811 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052811 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052811/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052811 Building REAL250005052812 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052812' /scratch/stefan/7921156/working/building/REAL250005052812 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052812 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052812/0 /scratch/stefan/7921156/working/building/REAL250005052812 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/972 `/scratch/stefan/7921156/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CCCC1) `REAL250005052812.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052812 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 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, 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: [80, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 82, 125, 125, 125, 143, 143, 143, 143, 143, 82, 82, 82, 82, 32, 32, 10, 1, 125, 429, 143, 143, 143, 143, 143, 143, 143, 143] 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]) total number of confs: 948 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: REAL250005052812 none CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 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, 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: [28, 8, 28, 85, 137, 137, 137, 143, 143, 143, 143, 143, 8, 1, 8, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 85, 85, 137, 143, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1] 429 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 517 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052812 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052812 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052812/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052812 Building REAL250005052813 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052813' /scratch/stefan/7921156/working/building/REAL250005052813 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052813 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052813/0 /scratch/stefan/7921156/working/building/REAL250005052813 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/973 `/scratch/stefan/7921156/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)COC1) `REAL250005052813.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052813 none CCC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)COC1 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', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 7, 7, 7, 36, 99, 100, 137, 137, 137, 143, 143, 143, 143, 143, 1, 1, 1, 3, 3, 3, 3, 3, 7, 36, 36, 100, 100, 100, 100, 137, 143, 1, 1, 1, 1] 143 rigid atoms, others: [1, 2, 3, 36, 37, 35, 18, 19, 20, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 568 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: REAL250005052813 none CCC1(C(=O)NCC(C)NC(=O)C2=CC(=O)[N-]O2)COC1 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', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 90, 90, 90, 44, 18, 9, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 143, 143, 143, 90, 44, 44, 18, 18, 18, 18, 9, 1, 143, 143, 143, 143] 143 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: 475 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052813 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052813 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052813/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052813 Building REAL250005052814 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052814' /scratch/stefan/7921156/working/building/REAL250005052814 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052814 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052814/0 /scratch/stefan/7921156/working/building/REAL250005052814 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/974 `/scratch/stefan/7921156/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(C)CCCO1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052814.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052814 none CC(CNC(=O)C1(C)CCCO1)NC(=O)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', '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, 8, 1, 11, 5, 5, 5, 5, 5, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [95, 51, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 95, 115, 115, 115, 117, 117, 117, 117, 117, 95, 95, 95, 95, 51, 51, 11, 2, 2, 2, 1, 1, 1, 1, 1, 1, 115, 117] 117 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 36, 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, 30, 37, 38]) total number of confs: 473 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: REAL250005052814 none CC(CNC(=O)C1(C)CCCO1)NC(=O)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', '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, 8, 1, 11, 5, 5, 5, 5, 5, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 17, 38, 85, 85, 85, 117, 117, 117, 117, 117, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 38, 38, 85, 117, 117, 117, 117, 117, 117, 117, 117, 117, 7, 1] 117 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: 396 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052814 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052814 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052814/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052814 Building REAL250005052815 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052815' /scratch/stefan/7921156/working/building/REAL250005052815 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052815 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052815/0 /scratch/stefan/7921156/working/building/REAL250005052815 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/975 `/scratch/stefan/7921156/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC(=O)N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052815.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052815 none CC(CNC(=O)C1CC(=O)N1)NC(=O)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.2', 'O.2', 'C.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, 5, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 6, 4, 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 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [144, 70, 13, 13, 1, 13, 1, 1, 1, 1, 1, 144, 176, 176, 176, 185, 185, 185, 185, 185, 144, 144, 144, 144, 70, 70, 13, 1, 1, 1, 1, 176, 185] 185 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27, 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, 31, 32]) total number of confs: 720 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: REAL250005052815 none CC(CNC(=O)C1CC(=O)N1)NC(=O)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.2', 'O.2', 'C.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, 5, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 6, 4, 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 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 58, 122, 122, 122, 185, 185, 185, 185, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 58, 58, 122, 185, 185, 185, 185, 10, 1] 185 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: 633 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052815 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052815 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052815/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052815 Building REAL250005052816 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052816' /scratch/stefan/7921156/working/building/REAL250005052816 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052816 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052816/0 /scratch/stefan/7921156/working/building/REAL250005052816 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/976 `/scratch/stefan/7921156/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H]1CCO[C@H]1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052816.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052816 none CC(CNC(=O)[C@H]1CCO[C@H]1C)NC(=O)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', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', '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, 12, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [45, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 45, 68, 68, 68, 71, 71, 71, 71, 71, 45, 45, 45, 45, 14, 14, 4, 1, 1, 1, 1, 2, 2, 2, 68, 71] 71 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 268 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: REAL250005052816 none CC(CNC(=O)[C@H]1CCO[C@H]1C)NC(=O)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', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', '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, 12, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 46, 68, 68, 68, 71, 71, 71, 71, 71, 71, 71, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 46, 46, 68, 71, 71, 71, 71, 71, 71, 71, 8, 1] 71 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: 259 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052816 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052816 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052816/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052816 Building REAL250005052817 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052817' /scratch/stefan/7921156/working/building/REAL250005052817 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052817 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052817/0 /scratch/stefan/7921156/working/building/REAL250005052817 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/977 `/scratch/stefan/7921156/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC(F)C1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052817.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052817 none CC(CNC(=O)C1CC(F)C1)NC(=O)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'] 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, 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 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [146, 61, 12, 12, 1, 12, 1, 1, 1, 1, 1, 147, 190, 190, 190, 198, 198, 198, 198, 198, 147, 147, 147, 147, 61, 61, 12, 1, 1, 1, 1, 1, 1, 190, 198] 198 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 27, 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, 33, 34]) total number of confs: 774 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: REAL250005052817 none CC(CNC(=O)C1CC(F)C1)NC(=O)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'] 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, 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 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [26, 11, 26, 73, 140, 140, 140, 198, 198, 198, 198, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 73, 73, 140, 198, 198, 198, 198, 198, 198, 11, 1] 198 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: 685 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052817 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052817 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052817/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052817 Building REAL250005052818 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052818' /scratch/stefan/7921156/working/building/REAL250005052818 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052818 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052818/0 /scratch/stefan/7921156/working/building/REAL250005052818 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/978 `/scratch/stefan/7921156/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)C(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052818.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052818 none CCC(O)C(C)C(=O)NCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [72, 70, 53, 70, 35, 53, 35, 35, 20, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 70, 210, 53, 53, 53, 53, 35, 20, 20, 10, 10, 10, 10, 4, 1] 216 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 529 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052818 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052818 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052818/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052818 Building REAL250005052819 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052819' /scratch/stefan/7921156/working/building/REAL250005052819 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052819 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052819/0 /scratch/stefan/7921156/working/building/REAL250005052819 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/979 `/scratch/stefan/7921156/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CC(=O)N1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052819.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052819 none CC(CNC(=O)CC1CC(=O)N1)NC(=O)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.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 129, 43, 43, 7, 43, 1, 1, 1, 1, 1, 1, 184, 201, 201, 201, 201, 201, 201, 201, 201, 184, 184, 184, 184, 129, 129, 43, 7, 7, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 30, 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, 34, 35]) total number of confs: 795 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052819 none CC(CNC(=O)CC1CC(=O)N1)NC(=O)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.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 4, 11, 34, 85, 85, 85, 183, 201, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 34, 34, 85, 183, 183, 201, 201, 201, 201, 4, 1] 201 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 781 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052819 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052819 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052819/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052819 Building REAL250005052820 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052820' /scratch/stefan/7921156/working/building/REAL250005052820 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052820 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052820/0 /scratch/stefan/7921156/working/building/REAL250005052820 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/980 `/scratch/stefan/7921156/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(O)C1CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052820.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052820 none CC(CNC(=O)C(O)C1CCC1)NC(=O)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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [188, 128, 33, 33, 5, 33, 1, 5, 1, 1, 1, 1, 188, 200, 200, 200, 201, 201, 201, 201, 201, 188, 188, 188, 188, 128, 128, 33, 5, 15, 1, 1, 1, 1, 1, 1, 1, 200, 201] 603 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38]) total number of confs: 824 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052820 none CC(CNC(=O)C(O)C1CCC1)NC(=O)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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 14, 36, 100, 100, 100, 177, 177, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 36, 36, 100, 177, 531, 201, 201, 201, 201, 201, 201, 201, 7, 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: 1303 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052820 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052820 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052820/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052820 Building REAL250005052821 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052821' /scratch/stefan/7921156/working/building/REAL250005052821 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052821 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052821/0 /scratch/stefan/7921156/working/building/REAL250005052821 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/981 `/scratch/stefan/7921156/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=NO1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005052821.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052821 none CC(CNC(=O)C1=CC=NO1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [67, 34, 8, 8, 1, 8, 1, 1, 1, 1, 1, 67, 90, 90, 90, 93, 93, 93, 93, 93, 67, 67, 67, 67, 34, 34, 8, 1, 1, 90, 93] 93 rigid atoms, others: [4, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 361 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: REAL250005052821 none CC(CNC(=O)C1=CC=NO1)NC(=O)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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [17, 8, 17, 43, 80, 80, 80, 93, 93, 93, 93, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 43, 43, 80, 93, 93, 8, 1] 93 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 311 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052821 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052821 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052821/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052821 Building REAL250005052822 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052822' /scratch/stefan/7921156/working/building/REAL250005052822 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052822 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052822/0 /scratch/stefan/7921156/working/building/REAL250005052822 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/982 `/scratch/stefan/7921156/working/3D/982' -> `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)C1) `REAL250005052822.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052822 none CCC(=O)N1CCC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 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, 7, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 18, 1, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 7, 18, 1, 1] 28 rigid atoms, others: [2, 4, 5, 6, 7, 8, 17, 23, 24, 25, 26, 27, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 28, 29]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052822 none CCC(=O)N1CCC(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 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, 7, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 26, 18, 26, 18, 18, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 28, 28, 28, 28, 28, 18, 18, 18, 18, 18, 8, 1, 18, 18] 28 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052822 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052822 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052822/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052822 Building REAL250005052823 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052823' /scratch/stefan/7921156/working/building/REAL250005052823 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052823 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052823/0 /scratch/stefan/7921156/working/building/REAL250005052823 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/983 `/scratch/stefan/7921156/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052823.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052823 none COCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [80, 46, 28, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 22, 22, 1, 81, 81, 81, 46, 46, 28, 28, 1, 1, 1, 1, 1, 7, 22, 1, 1] 116 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052823 none COCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 115, 99, 47, 22, 47, 22, 22, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 22, 116, 116, 116, 115, 115, 99, 99, 22, 22, 22, 22, 22, 7, 1, 22, 22] 116 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: 456 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052823 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052823 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052823/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052823 Building REAL250005052824 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052824' /scratch/stefan/7921156/working/building/REAL250005052824 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052824 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052824/0 /scratch/stefan/7921156/working/building/REAL250005052824 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/984 `/scratch/stefan/7921156/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2CC2)C1)C1=CC(=O)[N-]O1) `REAL250005052824.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052824 none O=C(NC1CCN(C(=O)C2CC2)C1)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.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 13, 13, 13, 13, 22, 22, 29, 29, 13, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 29, 29, 29, 29, 29, 13, 13, 1] 29 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052824 none O=C(NC1CCN(C(=O)C2CC2)C1)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.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 1, 6, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 1, 1, 13] 29 rigid atoms, others: [2, 3, 4, 5, 6, 7, 12, 20, 21, 22, 23, 24, 30, 31] set([0, 1, 32, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052824 none O=C(NC1CCN(C(=O)C2CC2)C1)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.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 15, 26, 29, 29, 29, 29, 29, 26, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 15, 15, 29] 29 rigid atoms, others: [7, 9, 10, 11, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052824 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052824 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052824/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052824 Building REAL250005052825 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052825' /scratch/stefan/7921156/working/building/REAL250005052825 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052825 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052825/0 /scratch/stefan/7921156/working/building/REAL250005052825 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/985 `/scratch/stefan/7921156/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2CCC2)C1)C1=CC(=O)[N-]O1) `REAL250005052825.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052825 none O=C(NC1CCN(C(=O)C2CCC2)C1)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', 'C.2', 'C.2', 'C.2', 'O.2', '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, 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, 7, 7, 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: [10, 1, 10, 10, 18, 18, 18, 18, 27, 27, 38, 38, 38, 18, 1, 1, 1, 1, 1, 1, 10, 18, 18, 18, 18, 18, 38, 38, 38, 38, 38, 38, 38, 18, 18, 1] 38 rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 119 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052825 none O=C(NC1CCN(C(=O)C2CCC2)C1)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', 'C.2', 'C.2', 'C.2', 'O.2', '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, 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, 7, 7, 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: [7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 1, 7, 18, 18, 18, 18, 18, 7, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1, 18] 38 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 13, 34, 21, 22, 23, 24, 25] set([0, 1, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052825 none O=C(NC1CCN(C(=O)C2CCC2)C1)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', 'C.2', 'C.2', 'C.2', 'O.2', '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, 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, 7, 7, 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: [34, 34, 19, 19, 19, 19, 7, 1, 7, 1, 1, 1, 1, 19, 34, 38, 38, 38, 38, 38, 34, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 19, 19, 38] 38 rigid atoms, others: [32, 7, 9, 10, 11, 12, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052825 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052825 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052825/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052825 Building REAL250005052826 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052826' /scratch/stefan/7921156/working/building/REAL250005052826 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052826 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052826/0 /scratch/stefan/7921156/working/building/REAL250005052826 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/986 `/scratch/stefan/7921156/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2CCCC2)C1)C1=CC(=O)[N-]O1) `REAL250005052826.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052826 none O=C(NC1CCN(C(=O)C2CCCC2)C1)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', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 14, 14, 14, 14, 28, 28, 36, 36, 36, 36, 14, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 14, 14, 1] 36 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: 111 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052826 none O=C(NC1CCN(C(=O)C2CCCC2)C1)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', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 1, 7, 14, 14, 14, 14, 14, 7, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 14] 36 rigid atoms, others: [2, 3, 4, 5, 6, 7, 14, 22, 23, 24, 25, 26, 37, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) 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: REAL250005052826 none O=C(NC1CCN(C(=O)C2CCCC2)C1)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', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 17, 33, 36, 36, 36, 36, 36, 33, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 36] 36 rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052826 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052826 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052826/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052826 Building REAL250005052827 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052827' /scratch/stefan/7921156/working/building/REAL250005052827 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052827 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052827/0 /scratch/stefan/7921156/working/building/REAL250005052827 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/987 `/scratch/stefan/7921156/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052827.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052827 none O=C(CC1CC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [41, 21, 41, 70, 78, 78, 21, 21, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 70, 70, 78, 78, 78, 78, 78, 21, 21, 21, 21, 21, 9, 1, 21, 21] 78 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: 288 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052827 none O=C(CC1CC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [15, 3, 1, 1, 1, 1, 15, 42, 42, 42, 42, 71, 71, 71, 78, 78, 78, 78, 78, 42, 3, 3, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 71, 78, 42, 42] 78 rigid atoms, others: [2, 3, 4, 5, 22, 23, 24, 25, 26] set([0, 1, 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]) 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: REAL250005052827 none O=C(CC1CC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 27, 42, 42, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 21, 21, 1, 27, 27, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 7, 21, 1, 1] 78 rigid atoms, others: [1, 34, 35, 6, 7, 8, 9, 10, 19, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052827 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052827 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052827/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052827 Building REAL250005052828 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052828' /scratch/stefan/7921156/working/building/REAL250005052828 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052828 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052828/0 /scratch/stefan/7921156/working/building/REAL250005052828 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/988 `/scratch/stefan/7921156/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(F)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052828.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052828 none CC(C)(F)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 14, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 6, 12, 1, 1] 28 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 19, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 32, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 31]) 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: REAL250005052828 none CC(C)(F)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 28, 28, 12, 21, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 28, 28, 28, 28, 28, 28, 12, 12, 12, 12, 12, 6, 1, 12, 12] 28 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052828 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052828 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052828/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052828 Building REAL250005052829 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052829' /scratch/stefan/7921156/working/building/REAL250005052829 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052829 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052829/0 /scratch/stefan/7921156/working/building/REAL250005052829 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/989 `/scratch/stefan/7921156/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052829.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052829 none CC(F)(F)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [21, 5, 21, 21, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 21, 21, 21, 1, 1, 1, 1, 1, 6, 17, 1, 1] 44 rigid atoms, others: [4, 6, 7, 8, 9, 10, 19, 23, 24, 25, 26, 27, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 28, 29]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052829 none CC(F)(F)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 27, 44, 44, 17, 27, 17, 17, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 44, 44, 44, 17, 17, 17, 17, 17, 6, 1, 17, 17] 44 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052829 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052829 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052829/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052829 Building REAL250005052830 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052830' /scratch/stefan/7921156/working/building/REAL250005052830 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052830 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052830/0 /scratch/stefan/7921156/working/building/REAL250005052830 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/990 `/scratch/stefan/7921156/working/3D/990' -> `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)C1) `REAL250005052830.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052830 none COCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [45, 26, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 1, 46, 46, 46, 26, 26, 1, 1, 1, 1, 1, 7, 20, 1, 1] 67 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 18, 24, 25, 26, 27, 28, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 29, 30]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052830 none COCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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, 38, 20, 38, 20, 20, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 67, 67, 67, 64, 64, 20, 20, 20, 20, 20, 8, 1, 20, 20] 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]) total number of confs: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052830 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052830 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052830/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052830 Building REAL250005052831 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052831' /scratch/stefan/7921156/working/building/REAL250005052831 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052831 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052831/0 /scratch/stefan/7921156/working/building/REAL250005052831 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/991 `/scratch/stefan/7921156/working/3D/991' -> `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)C1) `REAL250005052831.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052831 none CCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [38, 27, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 17, 17, 1, 40, 40, 40, 39, 39, 27, 27, 1, 1, 1, 1, 1, 7, 17, 1, 1] 71 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 32, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052831 none CCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 68, 37, 17, 37, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 71, 71, 71, 71, 71, 68, 68, 17, 17, 17, 17, 17, 8, 1, 17, 17] 71 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052831 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052831 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052831/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052831 Building REAL250005052832 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052832' /scratch/stefan/7921156/working/building/REAL250005052832 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052832 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052832/0 /scratch/stefan/7921156/working/building/REAL250005052832 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/992 `/scratch/stefan/7921156/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2=CC=CO2)C1)C1=CC(=O)[N-]O1) `REAL250005052832.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052832 none O=C(NC1CCN(C(=O)C2=CC=CO2)C1)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.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 8, 12, 6, 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, 3, 7, 7, 7, 7, 3, 7, 3, 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: [7, 1, 7, 7, 15, 15, 15, 15, 27, 27, 35, 35, 35, 35, 15, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 35, 35, 35, 15, 15, 1] 35 rigid atoms, others: [32, 1, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052832 none O=C(NC1CCN(C(=O)C2=CC=CO2)C1)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.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 8, 12, 6, 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, 3, 7, 7, 7, 7, 3, 7, 3, 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: [7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 1, 7, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 18, 18, 18, 1, 1, 15] 35 rigid atoms, others: [2, 3, 4, 5, 6, 7, 14, 22, 23, 24, 25, 26, 30, 31] set([0, 1, 32, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052832 none O=C(NC1CCN(C(=O)C2=CC=CO2)C1)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.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 8, 12, 6, 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, 3, 7, 7, 7, 7, 3, 7, 3, 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: [33, 33, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 18, 33, 35, 35, 35, 35, 35, 33, 18, 18, 18, 18, 18, 1, 1, 1, 18, 18, 35] 35 rigid atoms, others: [7, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052832 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052832 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052832/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052832 Building REAL250005052833 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052833' /scratch/stefan/7921156/working/building/REAL250005052833 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052833 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052833/0 /scratch/stefan/7921156/working/building/REAL250005052833 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/993 `/scratch/stefan/7921156/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052833.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052833 none CC(=O)NCC(=O)N1CCC(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 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, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 30, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 16, 16, 1, 72, 72, 72, 72, 30, 30, 1, 1, 1, 1, 1, 7, 16, 1, 1] 102 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 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: REAL250005052833 none CC(=O)NCC(=O)N1CCC(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 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, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 87, 36, 16, 36, 16, 16, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 102, 102, 102, 102, 87, 87, 16, 16, 16, 16, 16, 7, 1, 16, 16] 102 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 360 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052833 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052833 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052833/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052833 Building REAL250005052834 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052834' /scratch/stefan/7921156/working/building/REAL250005052834 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052834 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052834/0 /scratch/stefan/7921156/working/building/REAL250005052834 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/994 `/scratch/stefan/7921156/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052834.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052834 none CC(C)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 27, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 1, 27, 27, 27, 27, 27, 27, 27, 23, 23, 1, 1, 1, 1, 1, 7, 15, 1, 1] 50 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 19, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) 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: REAL250005052834 none CC(C)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 48, 50, 28, 15, 28, 15, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 48, 48, 15, 15, 15, 15, 15, 7, 1, 15, 15] 50 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: 198 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052834 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052834 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052834/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052834 Building REAL250005052835 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052835' /scratch/stefan/7921156/working/building/REAL250005052835 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052835 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052835/0 /scratch/stefan/7921156/working/building/REAL250005052835 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/995 `/scratch/stefan/7921156/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052835.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052835 none CC1CC1C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 29, 17, 29, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 41, 41, 41, 41, 41, 41, 41, 17, 17, 17, 17, 17, 8, 1, 17, 17] 41 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: 123 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052835 none CC1CC1C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 21, 39, 39, 39, 41, 41, 41, 41, 41, 21, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 39, 41, 21, 21] 41 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052835 none CC1CC1C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 17, 17, 1, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 7, 17, 1, 1] 41 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052835 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052835 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052835/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052835 Building REAL250005052836 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052836' /scratch/stefan/7921156/working/building/REAL250005052836 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052836 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052836/0 /scratch/stefan/7921156/working/building/REAL250005052836 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/996 `/scratch/stefan/7921156/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052836.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052836 none CCOCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 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] 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: [90, 76, 31, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 28, 28, 28, 28, 28, 1, 91, 90, 90, 91, 91, 31, 31, 1, 1, 1, 1, 1, 7, 28, 1, 1] 143 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 300 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: REAL250005052836 none CCOCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [143, 141, 117, 56, 28, 56, 28, 28, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 143, 143, 143, 143, 143, 117, 117, 28, 28, 28, 28, 28, 9, 1, 28, 28] 143 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: 471 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052836 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052836 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052836/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052836 Building REAL250005052837 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052837' /scratch/stefan/7921156/working/building/REAL250005052837 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052837 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052837/0 /scratch/stefan/7921156/working/building/REAL250005052837 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/997 `/scratch/stefan/7921156/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052837.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052837 none CC(C)=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 17, 17, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 7, 17, 1, 1] 42 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 32, 33]) 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: REAL250005052837 none CC(C)=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 17, 30, 17, 17, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 42, 42, 42, 42, 42, 42, 42, 17, 17, 17, 17, 17, 9, 1, 17, 17] 42 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: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052837 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052837 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052837/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052837 Building REAL250005052838 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052838' /scratch/stefan/7921156/working/building/REAL250005052838 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052838 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052838/0 /scratch/stefan/7921156/working/building/REAL250005052838 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/998 `/scratch/stefan/7921156/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2CCCO2)C1)C1=CC(=O)[N-]O1) `REAL250005052838.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052838 none O=C(NC1CCN(C(=O)C2CCCO2)C1)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', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 15, 15, 15, 15, 31, 31, 45, 45, 45, 45, 15, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 45, 45, 45, 45, 45, 45, 45, 15, 15, 1] 45 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: 141 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052838 none O=C(NC1CCN(C(=O)C2CCCO2)C1)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', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 1, 7, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 1, 1, 15] 45 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 14, 35, 22, 23, 24, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052838 none O=C(NC1CCN(C(=O)C2CCCO2)C1)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', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 28, 41, 45, 45, 45, 45, 45, 41, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 28, 28, 45] 45 rigid atoms, others: [32, 33, 7, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052838 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052838 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052838/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052838 Building REAL250005052839 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052839' /scratch/stefan/7921156/working/building/REAL250005052839 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052839 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052839/0 /scratch/stefan/7921156/working/building/REAL250005052839 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/999 `/scratch/stefan/7921156/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052839.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052839 none CSCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [73, 33, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 16, 16, 1, 73, 73, 73, 33, 33, 1, 1, 1, 1, 1, 7, 16, 1, 1] 104 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 18, 24, 25, 26, 27, 28, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 29, 30]) 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: REAL250005052839 none CSCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 83, 45, 16, 45, 16, 16, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 104, 104, 104, 83, 83, 16, 16, 16, 16, 16, 6, 1, 16, 16] 104 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: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052839 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052839 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052839/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052839 Building REAL250005052840 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052840' /scratch/stefan/7921156/working/building/REAL250005052840 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052840 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052840/0 /scratch/stefan/7921156/working/building/REAL250005052840 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1000 `/scratch/stefan/7921156/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052840.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052840 none CSCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [97, 38, 29, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 1, 98, 98, 98, 39, 39, 29, 29, 1, 1, 1, 1, 1, 7, 20, 1, 1] 158 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052840 none CSCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 98, 97, 45, 20, 45, 20, 20, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 158, 158, 158, 98, 98, 97, 97, 20, 20, 20, 20, 20, 9, 1, 20, 20] 158 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: 451 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052840 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052840 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052840/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052840 Building REAL250005052841 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052841' /scratch/stefan/7921156/working/building/REAL250005052841 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052841 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052841/0 /scratch/stefan/7921156/working/building/REAL250005052841 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1001 `/scratch/stefan/7921156/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052841.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052841 none CC(C)CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [51, 45, 56, 32, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 14, 14, 1, 56, 56, 51, 56, 56, 56, 56, 45, 45, 32, 32, 1, 1, 1, 1, 1, 7, 14, 1, 1] 96 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 40, 20, 39] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052841 none CC(C)CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 92, 96, 85, 38, 14, 38, 14, 14, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 96, 96, 96, 96, 96, 96, 96, 92, 92, 85, 85, 14, 14, 14, 14, 14, 6, 1, 14, 14] 96 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: 380 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052841 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052841 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052841/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052841 Building REAL250005052842 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052842' /scratch/stefan/7921156/working/building/REAL250005052842 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052842 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052842/0 /scratch/stefan/7921156/working/building/REAL250005052842 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1002 `/scratch/stefan/7921156/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2=CC=CN2)C1)C1=CC(=O)[N-]O1) `REAL250005052842.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052842 none O=C(NC1CCN(C(=O)C2=CC=CN2)C1)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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 6, 6, 15, 15, 15, 15, 36, 36, 60, 60, 60, 60, 15, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 15, 60, 60, 60, 60, 15, 15, 1] 60 rigid atoms, others: [1, 33, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 144 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052842 none O=C(NC1CCN(C(=O)C2=CC=CN2)C1)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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 1, 7, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 34, 34, 34, 34, 1, 1, 15] 60 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 14, 22, 23, 24, 25, 26, 31] set([0, 1, 33, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30]) total number of confs: 75 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: REAL250005052842 none O=C(NC1CCN(C(=O)C2=CC=CN2)C1)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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [58, 58, 34, 34, 34, 34, 11, 1, 11, 1, 1, 1, 1, 1, 34, 58, 60, 60, 60, 60, 60, 58, 34, 34, 34, 34, 34, 1, 1, 1, 1, 34, 34, 60] 60 rigid atoms, others: [7, 9, 10, 11, 12, 13, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 142 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052842 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052842 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052842/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052842 Building REAL250005052843 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052843' /scratch/stefan/7921156/working/building/REAL250005052843 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052843 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052843/0 /scratch/stefan/7921156/working/building/REAL250005052843 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1003 `/scratch/stefan/7921156/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2=COC=C2)C1)C1=CC(=O)[N-]O1) `REAL250005052843.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052843 none O=C(NC1CCN(C(=O)C2=COC=C2)C1)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.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 1, 1, 1, 11, 8, 12, 6, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 16, 16, 16, 16, 37, 37, 62, 62, 62, 62, 16, 1, 1, 1, 1, 1, 1, 8, 16, 16, 16, 16, 16, 62, 62, 62, 16, 16, 1] 62 rigid atoms, others: [32, 1, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 147 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052843 none O=C(NC1CCN(C(=O)C2=COC=C2)C1)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.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 1, 1, 1, 11, 8, 12, 6, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 1, 7, 16, 16, 16, 16, 16, 7, 1, 1, 1, 1, 1, 32, 32, 32, 1, 1, 16] 62 rigid atoms, others: [2, 3, 4, 5, 6, 7, 14, 22, 23, 24, 25, 26, 30, 31] set([0, 1, 32, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29]) total number of confs: 74 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: REAL250005052843 none O=C(NC1CCN(C(=O)C2=COC=C2)C1)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.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 1, 1, 1, 11, 8, 12, 6, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 32, 32, 32, 32, 11, 1, 11, 1, 1, 1, 1, 1, 32, 60, 62, 62, 62, 62, 62, 60, 32, 32, 32, 32, 32, 1, 1, 1, 32, 32, 62] 62 rigid atoms, others: [7, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32]) total number of confs: 150 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052843 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052843 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052843/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052843 Building REAL250005052844 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052844' /scratch/stefan/7921156/working/building/REAL250005052844 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052844 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052844/0 /scratch/stefan/7921156/working/building/REAL250005052844 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1004 `/scratch/stefan/7921156/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052844.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052844 none CCCCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 81, 50, 37, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 14, 14, 1, 116, 123, 123, 122, 122, 80, 81, 61, 61, 37, 37, 1, 1, 1, 1, 1, 7, 14, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 40, 20, 39] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) 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: REAL250005052844 none CCCCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 188, 140, 118, 37, 14, 37, 14, 14, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 197, 201, 201, 201, 201, 182, 186, 153, 153, 118, 118, 14, 14, 14, 14, 14, 6, 1, 14, 14] 201 rigid atoms, others: [38, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 943 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052844 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052844 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052844/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052844 Building REAL250005052845 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052845' /scratch/stefan/7921156/working/building/REAL250005052845 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052845 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052845/0 /scratch/stefan/7921156/working/building/REAL250005052845 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1005 `/scratch/stefan/7921156/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052845.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052845 none CC(C)(C)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [32, 22, 32, 32, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 1, 33, 33, 33, 32, 32, 32, 33, 32, 33, 22, 22, 1, 1, 1, 1, 1, 7, 20, 1, 1] 68 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 40, 20, 39] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 182 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: REAL250005052845 none CC(C)(C)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 67, 68, 68, 43, 20, 43, 20, 20, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 68, 68, 68, 68, 68, 68, 68, 68, 68, 67, 67, 20, 20, 20, 20, 20, 9, 1, 20, 20] 68 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: 236 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052845 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052845 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052845/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052845 Building REAL250005052846 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052846' /scratch/stefan/7921156/working/building/REAL250005052846 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052846 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052846/0 /scratch/stefan/7921156/working/building/REAL250005052846 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1006 `/scratch/stefan/7921156/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052846.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052846 none CCCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [77, 53, 37, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 18, 1, 78, 80, 80, 76, 77, 61, 61, 37, 37, 1, 1, 1, 1, 1, 7, 18, 1, 1] 130 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 19, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) 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: REAL250005052846 none CCCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 116, 104, 44, 18, 44, 18, 18, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 130, 130, 130, 130, 130, 116, 116, 104, 104, 18, 18, 18, 18, 18, 7, 1, 18, 18] 130 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: 538 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052846 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052846 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052846/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052846 Building REAL250005052847 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052847' /scratch/stefan/7921156/working/building/REAL250005052847 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052847 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052847/0 /scratch/stefan/7921156/working/building/REAL250005052847 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1007 `/scratch/stefan/7921156/working/3D/1007' -> `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)C1) `REAL250005052847.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052847 none CC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 7, 15, 1, 1] 21 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 32, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052847 none CC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 15, 21, 15, 15, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 21, 21, 21, 21, 21, 21, 21, 15, 15, 15, 15, 15, 8, 1, 15, 15] 21 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052847 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052847 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052847/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052847 Building REAL250005052848 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052848' /scratch/stefan/7921156/working/building/REAL250005052848 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052848 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052848/0 /scratch/stefan/7921156/working/building/REAL250005052848 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1008 `/scratch/stefan/7921156/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052848.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052848 none CCC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 7, 17, 1, 7, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 14, 14, 1, 22, 22, 22, 22, 22, 17, 17, 17, 17, 1, 1, 1, 1, 1, 7, 14, 1, 1] 44 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 19, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052848 none CCC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 42, 35, 42, 14, 35, 14, 14, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 44, 44, 44, 44, 44, 42, 42, 42, 42, 14, 14, 14, 14, 14, 6, 1, 14, 14] 44 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: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052848 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052848 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052848/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052848 Building REAL250005052849 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052849' /scratch/stefan/7921156/working/building/REAL250005052849 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052849 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052849/0 /scratch/stefan/7921156/working/building/REAL250005052849 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1009 `/scratch/stefan/7921156/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052849.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052849 none CCC(CC)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [27, 20, 7, 20, 25, 1, 7, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 11, 11, 1, 31, 31, 31, 31, 31, 20, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 7, 11, 1, 1] 61 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 40, 20, 39] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052849 none CCC(CC)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [57, 49, 34, 49, 54, 11, 34, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 57, 57, 57, 57, 57, 49, 54, 54, 54, 54, 54, 11, 11, 11, 11, 11, 5, 1, 11, 11] 61 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: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052849 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052849 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052849/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052849 Building REAL250005052850 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052850' /scratch/stefan/7921156/working/building/REAL250005052850 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005052850 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052850/0 /scratch/stefan/7921156/working/building/REAL250005052850 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1010 `/scratch/stefan/7921156/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2=NNC=C2)C1)C1=CC(=O)[N-]O1) `REAL250005052850.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052850 none O=C(NC1CCN(C(=O)C2=NNC=C2)C1)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.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 15, 15, 15, 15, 28, 28, 36, 36, 36, 36, 15, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 36, 36, 36, 15, 15, 1] 36 rigid atoms, others: [32, 1, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052850 none O=C(NC1CCN(C(=O)C2=NNC=C2)C1)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.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 1, 7, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 19, 19, 19, 1, 1, 15] 36 rigid atoms, others: [2, 3, 4, 5, 6, 7, 14, 22, 23, 24, 25, 26, 30, 31] set([0, 1, 32, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052850 none O=C(NC1CCN(C(=O)C2=NNC=C2)C1)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.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 19, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 19, 34, 36, 36, 36, 36, 36, 34, 19, 19, 19, 19, 19, 1, 1, 1, 19, 19, 36] 36 rigid atoms, others: [7, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052850 /scratch/stefan/7921156/working /scratch/stefan/7921156 mkdir: created directory `1' /scratch/stefan/7921156/working/building/REAL250005052850/1 /scratch/stefan/7921156/working/building/REAL250005052850 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 1 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1011 `/scratch/stefan/7921156/working/3D/1011' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2=CC=NN2)C1)C1=CC(=O)[N-]O1) `REAL250005052850.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005052850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052850/1/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', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052850 none O=C(NC1CCN(C(=O)C2=CC=NN2)C1)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.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 15, 15, 15, 15, 35, 35, 63, 63, 63, 63, 15, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 63, 63, 63, 15, 15, 1] 63 rigid atoms, others: [32, 1, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 148 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052850 none O=C(NC1CCN(C(=O)C2=CC=NN2)C1)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.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 1, 7, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 35, 35, 35, 1, 1, 15] 63 rigid atoms, others: [2, 3, 4, 5, 6, 7, 14, 22, 23, 24, 25, 26, 30, 31] set([0, 1, 32, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29]) total number of confs: 76 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: REAL250005052850 none O=C(NC1CCN(C(=O)C2=CC=NN2)C1)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.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 35, 35, 35, 35, 10, 1, 10, 1, 1, 1, 1, 1, 35, 61, 63, 63, 63, 63, 63, 61, 35, 35, 35, 35, 35, 1, 1, 1, 35, 35, 63] 63 rigid atoms, others: [7, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32]) total number of confs: 142 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052850 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052850 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052850/0.* 1: /scratch/stefan/7921156/working/building/REAL250005052850/1.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052850 Building REAL250005052851 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052851' /scratch/stefan/7921156/working/building/REAL250005052851 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052851 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052851/0 /scratch/stefan/7921156/working/building/REAL250005052851 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1012 `/scratch/stefan/7921156/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052851.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052851 none CSC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [43, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 1, 43, 43, 43, 18, 18, 18, 18, 1, 1, 1, 1, 1, 7, 13, 1, 1] 59 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052851 none CSC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 46, 33, 46, 13, 33, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 59, 59, 59, 46, 46, 46, 46, 13, 13, 13, 13, 13, 5, 1, 13, 13] 59 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: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052851 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052851 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052851/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052851 Building REAL250005052852 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052852' /scratch/stefan/7921156/working/building/REAL250005052852 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052852 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052852/0 /scratch/stefan/7921156/working/building/REAL250005052852 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1013 `/scratch/stefan/7921156/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052852.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052852 none CCOC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 39, 24, 7, 24, 1, 7, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 16, 16, 1, 40, 40, 40, 40, 40, 24, 24, 24, 24, 1, 1, 1, 1, 1, 7, 16, 1, 1] 68 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 142 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: REAL250005052852 none CCOC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 60, 35, 60, 16, 35, 16, 16, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 68, 68, 68, 68, 68, 60, 60, 60, 60, 16, 16, 16, 16, 16, 8, 1, 16, 16] 68 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: 236 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052852 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052852 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052852/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052852 Building REAL250005052853 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052853' /scratch/stefan/7921156/working/building/REAL250005052853 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052853 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052853/0 /scratch/stefan/7921156/working/building/REAL250005052853 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1014 `/scratch/stefan/7921156/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2=CNN=C2)C1)C1=CC(=O)[N-]O1) `REAL250005052853.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052853 none O=C(NC1CCN(C(=O)C2=CNN=C2)C1)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.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 17, 17, 17, 17, 34, 34, 35, 35, 35, 35, 17, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 35, 35, 35, 17, 17, 1] 35 rigid atoms, others: [32, 1, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 97 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052853 none O=C(NC1CCN(C(=O)C2=CNN=C2)C1)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.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 1, 7, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 20, 20, 20, 1, 1, 17] 35 rigid atoms, others: [2, 3, 4, 5, 6, 7, 14, 22, 23, 24, 25, 26, 30, 31] set([0, 1, 32, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29]) total number of confs: 63 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: REAL250005052853 none O=C(NC1CCN(C(=O)C2=CNN=C2)C1)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.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 19, 28, 30, 30, 30, 30, 30, 28, 19, 19, 19, 19, 19, 1, 1, 1, 19, 19, 30] 30 rigid atoms, others: [7, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32]) total number of confs: 70 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052853 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052853 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052853/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052853 Building REAL250005052854 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052854' /scratch/stefan/7921156/working/building/REAL250005052854 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052854 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052854/0 /scratch/stefan/7921156/working/building/REAL250005052854 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1015 `/scratch/stefan/7921156/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052854.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052854 none COCCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 71, 33, 27, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 1, 137, 137, 137, 67, 64, 40, 40, 27, 27, 1, 1, 1, 1, 1, 7, 13, 1, 1] 201 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052854 none COCCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 129, 109, 34, 13, 34, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 193, 193, 143, 143, 109, 109, 13, 13, 13, 13, 13, 4, 1, 13, 13] 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: 923 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052854 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052854 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052854/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052854 Building REAL250005052855 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052855' /scratch/stefan/7921156/working/building/REAL250005052855 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052855 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052855/0 /scratch/stefan/7921156/working/building/REAL250005052855 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1016 `/scratch/stefan/7921156/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2=NOC=C2)C1)C1=CC(=O)[N-]O1) `REAL250005052855.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052855 none O=C(NC1CCN(C(=O)C2=NOC=C2)C1)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.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 1, 1, 1, 11, 8, 12, 6, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 14, 14, 14, 14, 24, 24, 38, 38, 38, 38, 14, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 38, 38, 14, 14, 1] 38 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 96 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052855 none O=C(NC1CCN(C(=O)C2=NOC=C2)C1)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.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 1, 1, 1, 11, 8, 12, 6, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 1, 7, 14, 14, 14, 14, 14, 7, 1, 1, 1, 1, 1, 25, 25, 1, 1, 14] 38 rigid atoms, others: [2, 3, 4, 5, 6, 7, 14, 22, 23, 24, 25, 26, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 27, 28, 31]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052855 none O=C(NC1CCN(C(=O)C2=NOC=C2)C1)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.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 1, 1, 1, 11, 8, 12, 6, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 25, 25, 25, 25, 11, 1, 11, 1, 1, 1, 1, 1, 25, 36, 38, 38, 38, 38, 38, 36, 25, 25, 25, 25, 25, 1, 1, 25, 25, 38] 38 rigid atoms, others: [7, 9, 10, 11, 12, 13, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052855 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052855 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052855/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052855 Building REAL250005052856 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052856' /scratch/stefan/7921156/working/building/REAL250005052856 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052856 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052856/0 /scratch/stefan/7921156/working/building/REAL250005052856 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1017 `/scratch/stefan/7921156/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052856.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052856 none CCC=C(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [58, 32, 32, 7, 32, 1, 7, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 1, 58, 58, 58, 58, 58, 32, 32, 32, 32, 1, 1, 1, 1, 1, 7, 20, 1, 1] 95 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 241 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: REAL250005052856 none CCC=C(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 93, 93, 43, 93, 20, 43, 20, 20, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 95, 95, 95, 95, 95, 93, 93, 93, 93, 20, 20, 20, 20, 20, 9, 1, 20, 20] 95 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: 283 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052856 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052856 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052856/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052856 Building REAL250005052857 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052857' /scratch/stefan/7921156/working/building/REAL250005052857 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052857 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052857/0 /scratch/stefan/7921156/working/building/REAL250005052857 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1018 `/scratch/stefan/7921156/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052857.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052857 none COC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 26, 7, 26, 1, 7, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 11, 11, 1, 35, 35, 35, 26, 26, 26, 26, 1, 1, 1, 1, 1, 7, 11, 1, 1] 50 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 127 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: REAL250005052857 none COC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 50, 11, 32, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 5, 1, 11, 11] 50 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: 186 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052857 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052857 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052857/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052857 Building REAL250005052858 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052858' /scratch/stefan/7921156/working/building/REAL250005052858 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052858 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052858/0 /scratch/stefan/7921156/working/building/REAL250005052858 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1019 `/scratch/stefan/7921156/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052858.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052858 none CC(C)OCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 106, 127, 41, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 19, 19, 1, 127, 127, 127, 127, 127, 127, 127, 41, 41, 1, 1, 1, 1, 1, 7, 19, 1, 1] 201 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 381 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: REAL250005052858 none CC(C)OCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 128, 48, 19, 48, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 201, 201, 128, 128, 19, 19, 19, 19, 19, 6, 1, 19, 19] 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: 661 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052858 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052858 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052858/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052858 Building REAL250005052859 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052859' /scratch/stefan/7921156/working/building/REAL250005052859 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052859 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052859/0 /scratch/stefan/7921156/working/building/REAL250005052859 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1020 `/scratch/stefan/7921156/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052859.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052859 none CCCOCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 100, 50, 16, 2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 152, 152, 152, 152, 152, 100, 100, 16, 16, 1, 1, 1, 1, 1, 6, 10, 1, 1] 201 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 610 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052859 none CCCOCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 136, 74, 17, 10, 17, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 201, 201, 201, 201, 201, 183, 183, 74, 74, 10, 10, 10, 10, 10, 4, 1, 10, 10] 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: 740 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052859 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052859 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052859/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052859 Building REAL250005052860 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052860' /scratch/stefan/7921156/working/building/REAL250005052860 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052860 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052860/0 /scratch/stefan/7921156/working/building/REAL250005052860 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1021 `/scratch/stefan/7921156/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2CCOC2)C1)C1=CC(=O)[N-]O1) `REAL250005052860.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052860 none O=C(NC1CCN(C(=O)C2CCOC2)C1)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', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 5, 12, 12, 12, 12, 22, 22, 32, 32, 32, 32, 12, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 32, 32, 32, 32, 32, 32, 32, 12, 12, 1] 32 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: 104 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052860 none O=C(NC1CCN(C(=O)C2CCOC2)C1)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', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 1, 7, 12, 12, 12, 12, 12, 7, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 1, 1, 12] 32 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 14, 35, 22, 23, 24, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 36]) 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: REAL250005052860 none O=C(NC1CCN(C(=O)C2CCOC2)C1)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', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 16, 16, 16, 16, 6, 1, 6, 1, 1, 1, 1, 1, 16, 31, 32, 32, 32, 32, 32, 31, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16, 32] 32 rigid atoms, others: [32, 33, 7, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052860 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052860 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052860/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052860 Building REAL250005052861 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052861' /scratch/stefan/7921156/working/building/REAL250005052861 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052861 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052861/0 /scratch/stefan/7921156/working/building/REAL250005052861 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1022 `/scratch/stefan/7921156/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052861.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052861 none CCC(OC)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [34, 28, 7, 28, 36, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 39, 39, 39, 39, 39, 28, 36, 36, 36, 1, 1, 1, 1, 1, 6, 10, 1, 1] 68 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 224 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: REAL250005052861 none CCC(OC)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [62, 64, 33, 64, 67, 10, 33, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 67, 67, 67, 67, 67, 64, 67, 67, 67, 10, 10, 10, 10, 10, 4, 1, 10, 10] 68 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: 290 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052861 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052861 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052861/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052861 Building REAL250005052862 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052862' /scratch/stefan/7921156/working/building/REAL250005052862 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052862 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052862/0 /scratch/stefan/7921156/working/building/REAL250005052862 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1023 `/scratch/stefan/7921156/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052862.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052862 none COC(C)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [99, 80, 40, 79, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 17, 17, 1, 99, 99, 99, 80, 80, 80, 80, 40, 40, 1, 1, 1, 1, 1, 7, 17, 1, 1] 157 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) 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: REAL250005052862 none COC(C)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 126, 157, 46, 17, 46, 17, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 157, 157, 157, 157, 157, 157, 157, 126, 126, 17, 17, 17, 17, 17, 7, 1, 17, 17] 157 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: 630 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052862 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052862 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052862/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052862 Building REAL250005052863 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052863' /scratch/stefan/7921156/working/building/REAL250005052863 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052863 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052863/0 /scratch/stefan/7921156/working/building/REAL250005052863 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1024 `/scratch/stefan/7921156/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052863.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052863 none C=CCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [89, 50, 33, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 18, 1, 89, 89, 89, 50, 50, 33, 33, 1, 1, 1, 1, 1, 7, 18, 1, 1] 128 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052863 none C=CCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 108, 45, 18, 45, 18, 18, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 128, 128, 128, 128, 128, 108, 108, 18, 18, 18, 18, 18, 8, 1, 18, 18] 128 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: 497 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052863 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052863 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052863/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052863 Building REAL250005052864 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052864' /scratch/stefan/7921156/working/building/REAL250005052864 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052864 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052864/0 /scratch/stefan/7921156/working/building/REAL250005052864 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1025 `/scratch/stefan/7921156/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052864.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052864 none CCOCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 121, 62, 32, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 19, 19, 1, 127, 127, 127, 127, 127, 62, 62, 32, 32, 1, 1, 1, 1, 1, 7, 19, 1, 1] 201 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052864 none CCOCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 171, 123, 43, 19, 43, 19, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 171, 171, 123, 123, 19, 19, 19, 19, 19, 7, 1, 19, 19] 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: 757 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052864 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052864 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052864/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052864 Building REAL250005052865 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052865' /scratch/stefan/7921156/working/building/REAL250005052865 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052865 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052865/0 /scratch/stefan/7921156/working/building/REAL250005052865 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1026 `/scratch/stefan/7921156/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052865.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052865 none COCC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [58, 44, 22, 7, 22, 1, 7, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 18, 1, 58, 58, 58, 44, 44, 22, 22, 22, 22, 1, 1, 1, 1, 1, 7, 18, 1, 1] 87 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052865 none COCC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 73, 45, 73, 18, 45, 18, 18, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 87, 87, 87, 87, 87, 73, 73, 73, 73, 18, 18, 18, 18, 18, 7, 1, 18, 18] 87 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: 343 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052865 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052865 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052865/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052865 Building REAL250005052866 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052866' /scratch/stefan/7921156/working/building/REAL250005052866 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052866 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052866/0 /scratch/stefan/7921156/working/building/REAL250005052866 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1027 `/scratch/stefan/7921156/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052866.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052866 none C=CCOCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 95, 37, 12, 2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 19, 19, 1, 134, 134, 134, 95, 95, 12, 12, 1, 1, 1, 1, 1, 7, 19, 1, 1] 201 rigid atoms, others: [32, 35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 33, 34]) total number of confs: 505 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052866 none C=CCOCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 147, 87, 28, 19, 28, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 87, 87, 19, 19, 19, 19, 19, 6, 1, 19, 19] 201 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052866 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052866 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052866/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052866 Building REAL250005052867 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052867' /scratch/stefan/7921156/working/building/REAL250005052867 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052867 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052867/0 /scratch/stefan/7921156/working/building/REAL250005052867 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1028 `/scratch/stefan/7921156/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2=COC=N2)C1)C1=CC(=O)[N-]O1) `REAL250005052867.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052867 none O=C(NC1CCN(C(=O)C2=COC=N2)C1)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.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 1, 1, 1, 11, 8, 12, 6, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 15, 15, 15, 15, 27, 27, 33, 33, 33, 33, 15, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 33, 33, 15, 15, 1] 33 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 87 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052867 none O=C(NC1CCN(C(=O)C2=COC=N2)C1)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.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 1, 1, 1, 11, 8, 12, 6, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 1, 7, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 17, 17, 1, 1, 15] 33 rigid atoms, others: [2, 3, 4, 5, 6, 7, 14, 22, 23, 24, 25, 26, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 27, 28, 31]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052867 none O=C(NC1CCN(C(=O)C2=COC=N2)C1)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.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 1, 1, 1, 11, 8, 12, 6, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 17, 31, 33, 33, 33, 33, 33, 31, 17, 17, 17, 17, 17, 1, 1, 17, 17, 33] 33 rigid atoms, others: [7, 9, 10, 11, 12, 13, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052867 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052867 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052867/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052867 Building REAL250005052868 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052868' /scratch/stefan/7921156/working/building/REAL250005052868 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052868 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052868/0 /scratch/stefan/7921156/working/building/REAL250005052868 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1029 `/scratch/stefan/7921156/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052868.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052868 none CCCC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [43, 36, 20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 1, 43, 43, 43, 41, 43, 38, 38, 20, 20, 20, 20, 1, 1, 1, 1, 1, 7, 15, 1, 1] 73 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 40, 20, 39] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 215 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: REAL250005052868 none CCCC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 72, 62, 39, 62, 15, 39, 15, 15, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 73, 73, 73, 72, 73, 73, 73, 62, 62, 62, 62, 15, 15, 15, 15, 15, 8, 1, 15, 15] 73 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: 286 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052868 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052868 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052868/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052868 Building REAL250005052869 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052869' /scratch/stefan/7921156/working/building/REAL250005052869 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052869 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052869/0 /scratch/stefan/7921156/working/building/REAL250005052869 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1030 `/scratch/stefan/7921156/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1CC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052869.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052869 none O=C(CCC1CC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [48, 20, 48, 118, 127, 174, 174, 20, 20, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 118, 118, 130, 130, 174, 174, 174, 174, 174, 20, 20, 20, 20, 20, 9, 1, 20, 20] 174 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: 663 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052869 none O=C(CCC1CC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 1, 1, 1, 1, 36, 101, 101, 101, 101, 168, 168, 168, 174, 174, 174, 174, 174, 101, 7, 7, 3, 3, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 168, 174, 101, 101] 174 rigid atoms, others: [3, 4, 5, 6, 25, 26, 27, 28, 29] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052869 none O=C(CCC1CC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 41, 57, 101, 101, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 1, 41, 41, 67, 67, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 7, 20, 1, 1] 174 rigid atoms, others: [32, 1, 34, 33, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 472 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052869 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052869 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052869/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052869 Building REAL250005052870 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052870' /scratch/stefan/7921156/working/building/REAL250005052870 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052870 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052870/0 /scratch/stefan/7921156/working/building/REAL250005052870 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1031 `/scratch/stefan/7921156/working/3D/1031' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2CC=CC2)C1)C1=CC(=O)[N-]O1) `REAL250005052870.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052870 none O=C(NC1CCN(C(=O)C2CC=CC2)C1)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.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 13, 13, 13, 13, 18, 18, 27, 27, 27, 27, 13, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 13, 13, 1] 27 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: 87 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052870 none O=C(NC1CCN(C(=O)C2CC=CC2)C1)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.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 1, 7, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 13] 27 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 14, 35, 22, 23, 24, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 52 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: REAL250005052870 none O=C(NC1CCN(C(=O)C2CC=CC2)C1)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.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 1, 1, 12, 23, 27, 27, 27, 27, 27, 23, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 27] 27 rigid atoms, others: [32, 33, 7, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36]) total number of confs: 63 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052870 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052870 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052870/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052870 Building REAL250005052871 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052871' /scratch/stefan/7921156/working/building/REAL250005052871 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052871 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052871/0 /scratch/stefan/7921156/working/building/REAL250005052871 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1032 `/scratch/stefan/7921156/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052871.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052871 none O=C(CC1CCC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [49, 20, 49, 83, 107, 107, 107, 20, 20, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 83, 83, 107, 107, 107, 107, 107, 107, 107, 20, 20, 20, 20, 20, 8, 1, 20, 20] 107 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: 396 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052871 none O=C(CC1CCC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 7, 1, 1, 1, 1, 1, 34, 66, 66, 66, 66, 103, 103, 103, 107, 107, 107, 107, 107, 66, 7, 7, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 103, 107, 66, 66] 107 rigid atoms, others: [2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052871 none O=C(CC1CCC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 38, 66, 66, 66, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 1, 38, 38, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 7, 20, 1, 1] 107 rigid atoms, others: [32, 1, 34, 33, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052871 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052871 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052871/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052871 Building REAL250005052872 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052872' /scratch/stefan/7921156/working/building/REAL250005052872 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052872 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052872/0 /scratch/stefan/7921156/working/building/REAL250005052872 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1033 `/scratch/stefan/7921156/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1) `REAL250005052872.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052872 none CC(C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 10, 22, 22, 22, 22, 37, 37, 37, 40, 40, 40, 40, 40, 22, 1, 1, 1, 4, 4, 4, 4, 22, 22, 22, 22, 22, 37, 40, 22, 22, 1, 1, 1, 1, 1] 40 rigid atoms, others: [1, 34, 35, 36, 37, 38, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 106 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052872 none CC(C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 1, 21, 22, 22, 21, 21, 21, 21, 1, 1, 1, 1, 1, 7, 15, 1, 1, 22, 22, 22, 22, 22] 40 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 17, 25, 26, 27, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052872 none CC(C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 30, 15, 30, 15, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 40, 40, 40, 40, 40, 40, 40, 15, 15, 15, 15, 15, 7, 1, 15, 15, 40, 40, 40, 40, 40] 40 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052872 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052872 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052872/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052872 Building REAL250005052873 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052873' /scratch/stefan/7921156/working/building/REAL250005052873 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052873 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052873/0 /scratch/stefan/7921156/working/building/REAL250005052873 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1034 `/scratch/stefan/7921156/working/3D/1034' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052873.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052873 none CC=C(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 5, 18, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 18, 1, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 7, 18, 1, 1] 40 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052873 none CC=C(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 27, 40, 18, 27, 18, 18, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 40, 40, 40, 40, 40, 40, 40, 18, 18, 18, 18, 18, 8, 1, 18, 18] 40 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: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052873 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052873 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052873/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052873 Building REAL250005052874 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052874' /scratch/stefan/7921156/working/building/REAL250005052874 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052874 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052874/0 /scratch/stefan/7921156/working/building/REAL250005052874 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1035 `/scratch/stefan/7921156/working/3D/1035' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)N2CCC(NC(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005052874.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052874 none CC1CC(C(=O)N2CCC(NC(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 18, 30, 18, 18, 18, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 41, 41, 41, 41, 41, 41, 41, 41, 18, 18, 18, 18, 18, 8, 1, 18, 18, 41, 41] 41 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: 132 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052874 none CC1CC(C(=O)N2CCC(NC(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 22, 22, 22, 22, 38, 38, 38, 41, 41, 41, 41, 41, 22, 1, 2, 2, 2, 1, 1, 1, 1, 22, 22, 22, 22, 22, 38, 41, 22, 22, 1, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 20, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052874 none CC1CC(C(=O)N2CCC(NC(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 18, 1, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 7, 18, 1, 1, 22, 22] 41 rigid atoms, others: [32, 35, 4, 6, 7, 8, 9, 10, 19, 36, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 37, 38]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052874 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052874 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052874/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052874 Building REAL250005052875 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052875' /scratch/stefan/7921156/working/building/REAL250005052875 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052875 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052875/0 /scratch/stefan/7921156/working/building/REAL250005052875 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1036 `/scratch/stefan/7921156/working/3D/1036' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=C1CCC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052875.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052875 none O=C(C=C1CCC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [37, 17, 37, 53, 53, 53, 53, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 53, 53, 53, 53, 53, 53, 53, 17, 17, 17, 17, 17, 8, 1, 17, 17] 53 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: 147 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052875 none O=C(C=C1CCC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 9, 29, 29, 29, 29, 51, 51, 51, 53, 53, 53, 53, 53, 29, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 51, 53, 29, 29] 53 rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052875 none O=C(C=C1CCC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 29, 29, 29, 29, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 17, 17, 1, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 7, 17, 1, 1] 53 rigid atoms, others: [32, 1, 35, 36, 7, 8, 9, 10, 11, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 33, 34]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052875 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052875 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052875/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052875 Building REAL250005052876 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052876' /scratch/stefan/7921156/working/building/REAL250005052876 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052876 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052876/0 /scratch/stefan/7921156/working/building/REAL250005052876 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1037 `/scratch/stefan/7921156/working/3D/1037' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052876.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052876 none CC(C)=C(F)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [24, 24, 24, 6, 24, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 1, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 7, 15, 1, 1] 46 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 32, 33]) 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: REAL250005052876 none CC(C)=C(F)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 46, 29, 46, 15, 29, 15, 15, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 46, 46, 46, 46, 46, 46, 15, 15, 15, 15, 15, 8, 1, 15, 15] 46 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052876 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052876 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052876/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052876 Building REAL250005052877 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052877' /scratch/stefan/7921156/working/building/REAL250005052877 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052877 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052877/0 /scratch/stefan/7921156/working/building/REAL250005052877 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1038 `/scratch/stefan/7921156/working/3D/1038' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2=CCCC2)C1)C1=CC(=O)[N-]O1) `REAL250005052877.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052877 none O=C(NC1CCN(C(=O)C2=CCCC2)C1)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.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 1, 1, 1, 1, 1, 1, 8, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 13, 13, 1] 27 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: 69 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052877 none O=C(NC1CCN(C(=O)C2=CCCC2)C1)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.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 1, 7, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 1, 1, 13] 27 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 14, 35, 22, 23, 24, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 53 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: REAL250005052877 none O=C(NC1CCN(C(=O)C2=CCCC2)C1)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.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 16, 16, 16, 16, 8, 1, 8, 1, 1, 1, 1, 1, 16, 26, 27, 27, 27, 27, 27, 26, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16, 27] 27 rigid atoms, others: [32, 33, 7, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36]) total number of confs: 64 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052877 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052877 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052877/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052877 Building REAL250005052878 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052878' /scratch/stefan/7921156/working/building/REAL250005052878 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052878 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052878/0 /scratch/stefan/7921156/working/building/REAL250005052878 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1039 `/scratch/stefan/7921156/working/3D/1039' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC1C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052878.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052878 none CC1(C)CC1C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 24, 12, 24, 12, 12, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12, 12, 7, 1, 12, 12] 30 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052878 none CC1(C)CC1C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 28, 28, 28, 30, 30, 30, 30, 30, 16, 2, 2, 2, 2, 2, 2, 1, 1, 1, 16, 16, 16, 16, 16, 28, 30, 16, 16] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052878 none CC1(C)CC1C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 12, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 7, 12, 1, 1] 30 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052878 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052878 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052878/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052878 Building REAL250005052879 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052879' /scratch/stefan/7921156/working/building/REAL250005052879 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052879 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052879/0 /scratch/stefan/7921156/working/building/REAL250005052879 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1040 `/scratch/stefan/7921156/working/3D/1040' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C[C@@H]1C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052879.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052879 none CC1(C)C[C@@H]1C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 23, 30, 13, 23, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 13, 13, 7, 1, 13, 13] 30 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052879 none CC1(C)C[C@@H]1C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 14, 28, 28, 28, 30, 30, 30, 30, 30, 14, 1, 1, 1, 2, 2, 2, 1, 1, 14, 14, 14, 14, 14, 28, 30, 14, 14] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL250005052879 none CC1(C)C[C@@H]1C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [14, 14, 14, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 1, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 7, 13, 1, 1] 30 rigid atoms, others: [32, 33, 34, 37, 6, 8, 9, 10, 11, 12, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052879 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052879 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052879/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052879 Building REAL250005052880 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052880' /scratch/stefan/7921156/working/building/REAL250005052880 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052880 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052880/0 /scratch/stefan/7921156/working/building/REAL250005052880 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1041 `/scratch/stefan/7921156/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)[C@@H]2CCCO2)C1)C1=CC(=O)[N-]O1) `REAL250005052880.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052880 none O=C(NC1CCN(C(=O)[C@@H]2CCCO2)C1)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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 13, 13, 13, 13, 30, 30, 47, 47, 47, 47, 47, 13, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 47, 47, 47, 47, 47, 47, 13, 13, 1] 47 rigid atoms, others: [1, 36, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 139 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052880 none O=C(NC1CCN(C(=O)[C@@H]2CCCO2)C1)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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 7, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 1, 1, 13] 47 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 15, 35, 23, 24, 25, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052880 none O=C(NC1CCN(C(=O)[C@@H]2CCCO2)C1)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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 44, 47, 47, 47, 47, 47, 44, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 26, 26, 47] 47 rigid atoms, others: [32, 33, 7, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052880 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052880 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052880/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052880 Building REAL250005052881 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052881' /scratch/stefan/7921156/working/building/REAL250005052881 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052881 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052881/0 /scratch/stefan/7921156/working/building/REAL250005052881 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1042) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1042 `/scratch/stefan/7921156/working/3D/1042' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052881.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052881 none CCC(C)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [111, 85, 41, 86, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 18, 1, 111, 111, 111, 110, 111, 86, 86, 86, 86, 41, 41, 1, 1, 1, 1, 1, 7, 18, 1, 1] 178 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 40, 20, 39] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 532 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: REAL250005052881 none CCC(C)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 170, 141, 170, 47, 18, 47, 18, 18, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 178, 178, 178, 178, 178, 170, 170, 170, 170, 141, 141, 18, 18, 18, 18, 18, 7, 1, 18, 18] 178 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: 725 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052881 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052881 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052881/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052881 Building REAL250005052882 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052882' /scratch/stefan/7921156/working/building/REAL250005052882 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052882 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052882/0 /scratch/stefan/7921156/working/building/REAL250005052882 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1043) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1043 `/scratch/stefan/7921156/working/3D/1043' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052882.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052882 none C#CCCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 61, 40, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 1, 128, 123, 120, 71, 71, 40, 40, 1, 1, 1, 1, 1, 7, 13, 1, 1] 201 rigid atoms, others: [32, 35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 33, 34]) 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: REAL250005052882 none C#CCCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 126, 116, 39, 13, 39, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 201, 195, 188, 142, 142, 116, 116, 13, 13, 13, 13, 13, 5, 1, 13, 13] 201 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 917 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052882 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052882 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052882/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052882 Building REAL250005052883 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052883' /scratch/stefan/7921156/working/building/REAL250005052883 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052883 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052883/0 /scratch/stefan/7921156/working/building/REAL250005052883 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1044) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1044 `/scratch/stefan/7921156/working/3D/1044' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052883.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052883 none CC(C)(O)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 11, 18, 18, 3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 6, 6, 1, 19, 19, 19, 19, 18, 19, 54, 11, 11, 1, 1, 1, 1, 1, 5, 6, 1, 1] 69 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 149 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: REAL250005052883 none CC(C)(O)CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 23, 23, 8, 6, 8, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 23, 23, 23, 23, 23, 23, 69, 19, 19, 6, 6, 6, 6, 6, 3, 1, 6, 6] 69 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: 161 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052883 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052883 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052883/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052883 Building REAL250005052884 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052884' /scratch/stefan/7921156/working/building/REAL250005052884 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052884 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052884/0 /scratch/stefan/7921156/working/building/REAL250005052884 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1045) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1045 `/scratch/stefan/7921156/working/3D/1045' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052884.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052884 none CC(C)[C@@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [32, 23, 32, 7, 23, 23, 1, 7, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 14, 14, 1, 32, 32, 32, 32, 32, 32, 32, 69, 1, 1, 1, 1, 1, 7, 14, 1, 1] 180 rigid atoms, others: [32, 33, 34, 37, 6, 8, 9, 10, 11, 12, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 222 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: REAL250005052884 none CC(C)[C@@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [60, 52, 60, 32, 52, 52, 14, 32, 14, 14, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 60, 60, 60, 60, 60, 60, 60, 156, 14, 14, 14, 14, 14, 7, 1, 14, 14] 180 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 396 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052884 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052884 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052884/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052884 Building REAL250005052885 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052885' /scratch/stefan/7921156/working/building/REAL250005052885 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052885 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052885/0 /scratch/stefan/7921156/working/building/REAL250005052885 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1046) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1046 `/scratch/stefan/7921156/working/3D/1046' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052885.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052885 none CCC(C)=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [41, 22, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 19, 19, 1, 41, 41, 41, 41, 41, 22, 22, 22, 22, 1, 1, 1, 1, 1, 7, 19, 1, 1] 80 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) 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: REAL250005052885 none CCC(C)=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 56, 56, 56, 36, 19, 36, 19, 19, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 80, 80, 80, 80, 80, 56, 56, 56, 56, 19, 19, 19, 19, 19, 8, 1, 19, 19] 80 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: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052885 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052885 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052885/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052885 Building REAL250005052886 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052886' /scratch/stefan/7921156/working/building/REAL250005052886 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052886 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052886/0 /scratch/stefan/7921156/working/building/REAL250005052886 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1047) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1047 `/scratch/stefan/7921156/working/3D/1047' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C#CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052886.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052886 none CC(C)C#CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 12, 1, 1] 17 rigid atoms, others: [32, 35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 33, 34]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052886 none CC(C)C#CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 12, 17, 12, 12, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 7, 1, 12, 12] 17 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: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052886 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052886 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052886/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052886 Building REAL250005052887 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052887' /scratch/stefan/7921156/working/building/REAL250005052887 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052887 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052887/0 /scratch/stefan/7921156/working/building/REAL250005052887 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1048) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1048 `/scratch/stefan/7921156/working/3D/1048' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C#CC1CC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052887.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052887 none O=C(C#CC1CC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', '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, 1, 1, 5, 5, 5, 8, 5, 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: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 15, 20, 20, 20, 20, 20, 15, 15, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 20, 20, 20, 20, 20, 15, 15, 15, 15, 15, 8, 1, 15, 15] 20 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: 55 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052887 none O=C(C#CC1CC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', '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, 1, 1, 5, 5, 5, 8, 5, 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: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 18, 18, 18, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 18, 20, 6, 6] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052887 none O=C(C#CC1CC1)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', '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, 1, 1, 5, 5, 5, 8, 5, 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: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 1, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 7, 15, 1, 1] 20 rigid atoms, others: [1, 34, 33, 7, 8, 9, 10, 11, 20, 26, 27, 28, 29, 30] set([0, 32, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052887 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052887 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052887/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052887 Building REAL250005052888 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052888' /scratch/stefan/7921156/working/building/REAL250005052888 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052888 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052888/0 /scratch/stefan/7921156/working/building/REAL250005052888 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1049) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1049 `/scratch/stefan/7921156/working/3D/1049' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005052888.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052888 none C=C(C)CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [77, 50, 77, 39, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 16, 16, 1, 77, 77, 77, 77, 77, 50, 50, 39, 39, 1, 1, 1, 1, 1, 7, 16, 1, 1] 118 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052888 none C=C(C)CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 113, 118, 101, 42, 16, 42, 16, 16, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 118, 118, 118, 118, 118, 113, 113, 101, 101, 16, 16, 16, 16, 16, 7, 1, 16, 16] 118 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: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052888 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052888 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052888/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052888 Building REAL250005052889 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052889' /scratch/stefan/7921156/working/building/REAL250005052889 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052889 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052889/0 /scratch/stefan/7921156/working/building/REAL250005052889 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1050) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1050 `/scratch/stefan/7921156/working/3D/1050' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)N2CCC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1) `REAL250005052889.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052889 none CC1(C(=O)N2CCC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 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, 22, 8, 22, 8, 8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 5, 1, 8, 8, 23, 23, 23, 23] 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: 61 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052889 none CC1(C(=O)N2CCC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 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: [1, 1, 1, 4, 4, 12, 12, 12, 12, 21, 21, 21, 23, 23, 23, 23, 23, 12, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 21, 23, 12, 12, 1, 1, 1, 1] 23 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 18, 19] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 60 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: REAL250005052889 none CC1(C(=O)N2CCC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 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: [12, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 1, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 1, 1, 12, 12, 12, 12] 23 rigid atoms, others: [2, 4, 5, 6, 7, 8, 17, 23, 24, 25, 26, 27, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 28, 29, 32, 33, 34, 35]) total number of confs: 48 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052889 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052889 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052889/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052889 Building REAL250005052890 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052890' /scratch/stefan/7921156/working/building/REAL250005052890 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052890 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052890/0 /scratch/stefan/7921156/working/building/REAL250005052890 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1051) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1051 `/scratch/stefan/7921156/working/3D/1051' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)[C@H]2CCCO2)C1)C1=CC(=O)[N-]O1) `REAL250005052890.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052890 none O=C(NC1CCN(C(=O)[C@H]2CCCO2)C1)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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 7, 7, 15, 15, 15, 15, 34, 34, 43, 43, 43, 43, 43, 15, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 43, 43, 43, 43, 43, 43, 15, 15, 1] 43 rigid atoms, others: [1, 36, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 127 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052890 none O=C(NC1CCN(C(=O)[C@H]2CCCO2)C1)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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 7, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 1, 1, 15] 43 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 15, 35, 23, 24, 25, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052890 none O=C(NC1CCN(C(=O)[C@H]2CCCO2)C1)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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 37, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 37, 43, 43, 43, 43, 43, 37, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 20, 20, 43] 43 rigid atoms, others: [32, 33, 7, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052890 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052890 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052890/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052890 Building REAL250005052891 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052891' /scratch/stefan/7921156/working/building/REAL250005052891 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052891 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052891/0 /scratch/stefan/7921156/working/building/REAL250005052891 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1052) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1052 `/scratch/stefan/7921156/working/3D/1052' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2=NNN=C2)C1)C1=CC(=O)[N-]O1) `REAL250005052891.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052891 none O=C(NC1CCN(C(=O)C2=NNN=C2)C1)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.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 15, 27, 27, 39, 39, 39, 39, 15, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 15, 39, 39, 15, 15, 1] 39 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 102 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052891 none O=C(NC1CCN(C(=O)C2=NNN=C2)C1)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.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 1, 7, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 25, 24, 1, 1, 15] 39 rigid atoms, others: [2, 3, 4, 5, 6, 7, 14, 22, 23, 24, 25, 26, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 27, 28, 31]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052891 none O=C(NC1CCN(C(=O)C2=NNN=C2)C1)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.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 25, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 24, 36, 39, 39, 39, 39, 39, 36, 25, 25, 25, 25, 25, 1, 1, 25, 25, 39] 39 rigid atoms, others: [7, 9, 10, 11, 12, 13, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052891 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052891 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052891/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052891 Building REAL250005052892 mkdir: created directory `/scratch/stefan/7921156/working/building/REAL250005052892' /scratch/stefan/7921156/working/building/REAL250005052892 /scratch/stefan/7921156/working /scratch/stefan/7921156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005052892 mkdir: created directory `0' /scratch/stefan/7921156/working/building/REAL250005052892/0 /scratch/stefan/7921156/working/building/REAL250005052892 /scratch/stefan/7921156/working /scratch/stefan/7921156 Protomer 0 (index: 1053) Found valid previously generated 3D confromation in /scratch/stefan/7921156/working/3D/1053 `/scratch/stefan/7921156/working/3D/1053' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CC(=O)N2CCC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1) `REAL250005052892.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005052892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921156/working/building/REAL250005052892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052892 none CC1(CC(=O)N2CCC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 97, 42, 18, 42, 18, 18, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 128, 128, 128, 128, 128, 97, 97, 18, 18, 18, 18, 18, 7, 1, 18, 18, 128, 128, 128, 128] 128 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: 480 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005052892 none CC1(CC(=O)N2CCC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 9, 35, 35, 78, 78, 78, 78, 121, 121, 121, 128, 128, 128, 128, 128, 78, 1, 1, 2, 2, 2, 9, 9, 78, 78, 78, 78, 78, 121, 128, 78, 78, 1, 1, 1, 1] 128 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 19, 20] set([3, 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: 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: REAL250005052892 none CC1(CC(=O)N2CCC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [78, 38, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 18, 1, 78, 78, 78, 78, 78, 38, 38, 1, 1, 1, 1, 1, 7, 18, 1, 1, 78, 78, 78, 78] 128 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 31, 32, 35, 36, 37, 38]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921156/working/building/REAL250005052892 /scratch/stefan/7921156/working /scratch/stefan/7921156 Finished preparing REAL250005052892 Recording results /scratch/stefan/7921156/working /scratch/stefan/7921156 Appending to /scratch/stefan/7921156/finished/xaaaaao.* 0: /scratch/stefan/7921156/working/building/REAL250005052892/0.* Removing working files in /scratch/stefan/7921156/working/building/REAL250005052892 /scratch/stefan/7921156 Compressing combined databse files /scratch/stefan/7921156/finished/xaaaaao.db2.gz /scratch/stefan/7921156/finished/xaaaaao.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7921156/finished) ======================================================= Finalizing... removed `/scratch/stefan/7921156/working/3D/1054' removed directory: `/scratch/stefan/7921156/working/3D' `/scratch/stefan/7921156/working/protonate' -> `/scratch/stefan/7921156/archive' `/scratch/stefan/7921156/working/input-smiles.ism' -> `/scratch/stefan/7921156/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7921156/working/building' rmdir: removing directory, `/scratch/stefan/7921156/working' ls: No match. ls: No match.